I actually have a complete ss installation in a sub directory of a ss installation. To make sure the top ss installation passes all requests for the lower one I have the following .htaccess file in the top ss installation:
The RewriteRules means that any request coming in that starts with /familytrees is passed through to the lower ss installation in the familytrees subdirectory. All other requests are handled by the normal ss handler.
Check out www.pyenet.co.nz and www.pyenet.co.nz/familytrees to see the effect.