I found that I actually had to create a different data source connections for each RQM project.

1. Open XML data Configuration Lite application on the RCR server.

(need to repeat the below steps for each of the files listed below.).
/dataconfig/configs/Configurations
/dataconfig/configs/live data config

2. Click File > Open Configuration and select the configuration file
3. Click File > New Resource Group
4. Give the new resource group a name (I use the name of the project in RQM).
5. Copy the rest of the information from the default RQM data source connection.
6. In the Relative Path URL, remove the words Quality+Manager at the end and replace them with your RQM project area name. Use + instead of spaces if you have spaces in your RQM project area name.
7. Run the RQMAll data movement task from http://:9080/insight.

I find this to be rather cumbersome, but have not had any one point out another way to do it. This way means that every time a new project area gets created in RQM, a new data source connection needs to be added to the reporting server.

If someone knows of a better way to do this, or a root URL to use instead of the individual project areas, I would appreciate it.