Well, you can add this line to the login script of the users:
NET USE * /DELETE /Y
That line will run through and delete all mapped drives automatically. So, if that is ran when the users first log in, and then after that you map the one drive letter to the applications folder, then there will be all of those free drive letters for the app to use in the future.
Then when the users log off and log back in the next day, the logon script deletes all the old mapped drives, and you start the process over again.
You can also use the NET USE command in a stand-along BAT file itself. So, you could make a BAT file that does the NET USE command I listed above, then a NET USE to map a single drive letter to your application folder, and that is it. Here is what I mean (for an example):
NET USE * /DELETE /Y
NET USE L: \\SERVER1\APPLICATIONFOLDER
call L:\YOURAPPLICATION.EXE
hope this helps