Here is a relevant thread:
DOS RAM limiter?

edit: I seem to recall that you can just right-click your MS-DOS Mode icon and make some changes there to limit your DOS session to 64MB or less.

edit2: I think this is what I was thinking of. still some very useful info in here, you should go through it if you haven't yet:
Phil's MS-DOS Mode Tutorial: Working Memory, Mouse, CD-ROM and Sound Blaster 16/32/64 in Windows 9x MS-DOS Mode