If your subway doesn't out of the ground anywhere (ie it's completely submerged) there is no reason to burry any part of the map under the baseboard. just lay all your tracks on the baseboard. Doing it this way is easier for you to layout & easier for the users to navigate when setting up their sessions. Download and take a look at how the U7 subway map is made here:
http://www.trainz-multiplayer.de/download/index.php/Entry/180-Berliner-U7-Version-2-0/
If you're map does have surface or elevated trackage as well, you can use a dig-hole (andi-06 makes a good one) to cut a hole in the baseboard where needed (10m minimum) to get your tracks thru. Any track-type tunnel already has a dig-hole built in.
peter
PS: I think with the ProTrainz kit you have to lay them out on the ground then lower them underground.