Installing RS instance in native mode plus for SharePoint-Collection of common programming errors

Hi pscorca,

You can refer to the article below, which is related to SQL Server 2005, there is not too much difference with SQL Server 2008 R2 in multiple instances of Reporting services installation:
Installing Multiple Instances of Reporting Services

Another article which related to SQL Server 2008 R2 Report Server Scale-Out Deployment, but it involved multiple instances of Reporting services installation, I think it can give you some enlighten.

How to: Configure a Report Server Scale-Out Deployment (Reporting Services Configuration)

Thanks,
Bill Lu