Hi

We completed the installation of SCCM 2012 R2. SSRS is configured on a dedicated server and SQL DBs configured on a failover cluster.  With SQL / SSRS we have 2 instances, one for SCCM & VMM and second for SCOM. Reporting with SCOM has been completed with 2nd instance and now looking to get a support / KB article to complete the reporting for SCCM 2012 R2.

Thanks in advance

https://technet.microsoft.com/en-us/library/gg682077.aspx#BKMK_SiteSystemRolePrereqs and https://technet.microsoft.com/en-us/library/hh272770.aspx.

Sorry, this didn't help me to configure Reporting services role. I found some articles, but no-where it's clearly provided in-detail. As mentioned before, we have 2 SQL instances (one for SCCM / VMM) and second for SCOM. SSRS is configured on a standalone server and configured 2 reporting instances against each instance of SQL DB. SCOM reporting has been configured with DB instance 2 and it's working fine.

Our concern is while we confgure the Reporting Service role, we mention the SSRS server and DB instance1 with SCCM 2012 R2, will this affect SCOM reporting servicves any way (even though it's with instance 2)? Also do we need to select the option Require the site server to initiate connection to site system

Once we provided above info we selected the Reporting Services Point and as seen below it populated the SQL DB server name \ instance 1 and with correct SSCM DB. The folder it's creating on reporting server is a DB folder or Windows folder? Also what kind of permissions do we need to provide for reporting services account (as of now we mentioned sccm admin account which is member of domain admins as service account with reporting service / db instance1 on SSRS server).

Are the above steps looks fine? Already both SQL nodes and SQL cluter instance 1 is showing as site system servers

Thank You

"Require the site server to initiate connection to site system" is most likely not needed. 
Examine srsrp.log to get more information about the reporting services point. The ConfigMgr folders are created on the SRS server (http://SRS/Reports). The account needs datareader rights.