Chris,
1. There are (were) 2 Loops on the Lower Level, the Inside and the Outside. The Outside serviced the Madison Ave. Yard and could handle any type of equipment. The Inner was located at the east (south) end of the platforms, was much tighter, and could be used only by the original NYC heavyweight MU's.
2. The preferred handling of the nYC long-distance trains which were serviced at MO was via the Upper Level Loop tracks. These were the last part of GCT to be completed and were referred to as the "Arrivals Station". However, in peak hours the limited capacity of the tracks and the length of time required to unload a long-distance train meant that many trains went to a stub-end platform. Also, there were some commuter consists and NH trains that went to MO for storage.
3. There were (are) stairways between the levels to allow employees of various departments easy access. Upper Level Yard tracks were accessed off the Upper Level.
What may be confusing is that the book does not show the actual number of trackage levels: Upper Level; Upper Level Loop; Lower Level; and Lower Level Loop.
4. Arriving at GCT, the 4 Main Tracks ended at Tower U at E. 56th St. Going into the Terminal, there were 10 tracks: A, B. F, and J to the Lower Level; C, D, E, G, H, and I to the Upper Level. Downtstairs, Tower B controlled access to the platforms; Upstairs, it was Tower A.
Hope this helps.