The System Center documentation clearly states you must use a separate instance of Reporting Services for each component of the suite.  Well, that’s fine, but you don’t want to have multiple Reporting Services servers just for reporting.  In my series of posts that outline how to install SQL for System Center 2016 (links below), we used a 4 box configuration that you can see in the diagram below.  In this article, we will install another instance of Reporting Services on the two Reporting Services servers.  The same process can be used if you are using Reporting Services collocated on the SQL Servers.
Installing SQL for System Center 2016 Posts
Diagram of Setup
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Installing a new Reporting Services Instances
You can install multiple instances of Microsoft SQL Server Reporting Services on the same computer. Each instance will have its own report server database, configuration files, and virtual directories. One instance can be the default instance. All other instances must be named instances. A server can run multiple instances of Reporting Services at the same time, and each instance runs independently of the other instances.
Install an additional Reporting Services instance on the computer that is running Reporting Services. To install additional instances, you must run the SQL Server Setup Wizard one time for each report server instance that you want to install. You cannot install multiple instances at the same time.
When you install multiple report server instances on the same computer, each additional instance must be installed as a named instance. To install an additional, named instance, you must run the SQL Server Setup Wizard again.
Insert the SQL Server Media and run setup.exe
Click Install and then click New SQL Server stand-alone installation or add features to an existing installation
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Select Microsoft Update if you wish and click Next
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Continue through the wizard until you reach the Installation Type screen and ensure Perform a new installation of SQL Server 2016 is selected and click Next
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Enter your Product Key or click Specify a free edition for a 180 free trial
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Click I accept the licence terms and click Next
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Select Reporting Services – Native and click Next
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Enter a name for the Reporting instance and click Next
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Enter your SQL Service Account credential and click Next
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On the Configuration screen you will see we have no option than to Install only.  Therefore, click Next
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Click Install
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Once setup is complete click Close
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Now do exactly the same process on the second Report Server if you have a HA deployment.

Configuring the second SQL Server 2016 Reporting Services instance
From the Start Menu open the Reporting Services Configuration Manager
On the Connection Screen select the new Reporting Services Instance and Click Connect
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Click Web Service URL then click Apply to accept the defaults
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You should see success in the Results pane
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Now click on Database then click Change Database
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Click Create a new report server database and click Next
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Enter the name of your AlwaysOn Availability group LISTENER or SQL Server if you have just one and click Test Connection and ensure it succeeds.  Then click Next
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The default name is ReportServer but as this is a second instance that name will be taken so change it to something relevant and click Next
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Accept the defaults for the credentials and click Next
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On the Summary click Next
Once the wizard has ran and everything was successful click Finish
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Click the Web Portal URL link. Accept all the default values and click Apply
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Verify that the reporting services instance is configured and working properly. You can do this by opening a web browser and accessing the URL defined in the Web Portal URL page
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Now we have a second instance of  SQL Server 2016 Reporting Services working for the first node we need to add the second node if you have one.

Configuring the second SQL Server 2016 Reporting Services Server
Log onto the second Reporting Services / SQL server.
From the Start Menu open the Reporting Services Configuration Manager
On the Connection Screen select the new Reporting Services Instance and Click Connect
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Click Web Service URL then click Apply to accept the defaults
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You should see success in the Results pane
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Do the same on the Web Portal URL.
Click the Database link and click the Change Database button. This will open the Report Server Database Configuration Wizard
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Select the Choose an existing report server database option and click Next
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Enter the name of your AlwaysOn Availability group LISTENER or SQL Server and click Test Connection and ensure it succeeds.  Then click Next
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Select your new ReportServer instance database from the drop down menu and click Next
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Accept the defaults for the credentials and click Next
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On the Summary click Next
Once the wizard has ran and everything was successful click Finish
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Join the second SQL Server 2016 Reporting Services instance to the Scale-Out Deployment
In the past, you may not have paid attention to the last link in the Reporting Services Configuration Manager – the Scale-Out Deployment link. When you click on that link, you should see a message stating that you should connect to the report server that has already been joined to this scale-out deployment.
Click Scale-out Deployment
When you click on that link, you should see a message stating that you should connect to the report server that has already been joined to this scale-out deployment
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This means that we need to connect to the first Reporting Services Server that we configured and accept the second reporting services instance to join the scale-out deployment.
On the first Reporting Services Server in Reporting Services Configuration Manager click Add Server
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The server should now successfully of joined the web farm
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Go back to the second Reporting Services Server and Click the Web Portal URL link. Accept all the default values and click Apply
Now test to ensure you can navigate to the Web Portal URL
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Encyption Keys
We now need to ensure that the encryption key from the first node is restored on the second node to be able to share encrypted data between the two.
On the Report Server Configuration Manager click Encryption Keys.  Click Backup and save it on your network that can be access by the second Reporting Services Server.
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Now restore the key on the second Reporting Services Server

Final Test
Now the installation and configuration is all complete, all that there is left to do is to test the Load Balanced URL.  Navigate to http://loadbalanceddnsname/Reports
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Adding DB’s to the AlwaysOn Cluster
One thing the wizards don’t do is add the Databases to the cluster therefore lets do this.
Open SQL Management Studio on the first SQL server and expand Databases.  Right click the new reporting instance database and click Properties and select Options and ensure the Recovery model is set to Full.
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Closer the properties window and right click the new reporting instance database Tasks > Backup
Click Add and specify the backup location then click OK
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Right click the Availability Group and click Add Database
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Once the wizard opens click Next on the Introduction screen and On the Select Databases screen select the ReportServer which should state “Meets prerequisites” then click Next
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On the Select Initial Data Synchronization step enter a File Share location on your network and click Next
On the Connect to Existing Secondary Replicas step click Connect and connect to the secondary SQL Server and click Next
Ensure the validation passes and click Next
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Then click Finish and the ReportServer database should now be added to the AlwaysOn Availability group
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Now do the same with the ReportServerTempDB
That’s it, you now have a second Reporting Services instance for one of your System Center components.