The track map from world.nycsubway.org that you linked in the other thread pretty much illustrates the Gov't Center track layout. Basically, there are two loops, one oriented towards each direction, that are situated on top of each other.
If you have a chance to visit again -- when on the northbound (Lechmere) platform, look up the track towards Haymarket. You can see the switch and signal for the loop that the GC turnback trains use to head west again. As soon as they leave the Lechmere-bound track, they cross the Brattle Loop track, then curve off and begin to run roughly parallel to the westbound main track and the Brattle Loop, before finally crossing the Brattle Loop track again, joining the westbound (Park St. bound) main track, and entering back into GC station on the other side, headed towards the western end of the Green Line branches.
Wondering if I'll see the Western Route double-tracking finished before I retire...
Photo: Melbourne W7 No. 1019 on Route 78, Bridge & Church Streets, Richmond, Victoria. 10/21/2010