How should I deploy these SSRS reports?
Well... I figured it out!

Here's what I did:


Deploy all the reports from the BIDS project to a main folder, say Source Reports.
On the ReportServer, create site-specific folders in another folder, say Site-Specific Reports.  Also in that folder, create a Master Reports folder.
Copy the Master reports to the Master Reports folder.
For each site report, create a linked report in their site-specific folder under Site-Specific Reports.


Now here's the "tricky" part... if you edit the report in the Source Reports folder in Report Builder, you can set up the sub-report to point to a specific folder structure on the ReportServer.  This enables you to use sub-reports anywhere on your ReportServer, not just in the same local directory.  My assumption is you can also type in the full path of the deployed report you wish to use as a sub-report into BIDS, but with Report Builder you can browse and click.

So, in this case, I have made all of the site-specific reports point to the Master report in the Master Reports folder.

This is a great solution for us.  Now we can grant user access at the folder level without creating excessive burden on the report deployment process.