The IMS and RMS are two different and separate things. The Rear Main Seal is on the crankshaft. The Intermediate shaft is BELOW the crankshaft.
In the attached pic, the blue is the RMS, and the red is the IMS.
For a better explanation check out Wayne Dempsey's excellent article on Pelican Parts:
http://www.pelicanparts.com/techarticles/Boxster_Tech/13-ENGINE-Common_Engine_Failures/13-ENGINE-Common_Engine_Failures.htm
So, as the tranny bolts up tight to the back of the engine, you can't tell which one is leaking.