You should not experience any problems from not using the root drive mapping or logon scripts. These are only meant to help you configure a user and give him/her access to anything he/she may need. You can use the root drive mapping to give the user a home folder where he or she may store all of their personal data. You may use logon scripts to map them to printers, shared folders, and lots of other things can be done with scripts. Check out these links:
Look at the section entitled "Specify a Home Directory For a Terminal Server"
If you want to use a logon script, you will have to find and use commands that are compatible with the operating system your user's are logging onto. Remember, without using Group Policy (and that gets in depth) you will only be able to assign one logon script per user. Enter that login script name (make sure you enter the .bat or .cmd extension with the name) in the Profile Tab under Active Directory User's and Computers and make sure you save that script file you created in the netlogon share (depends on your OS also) of one of your domain controllers.
As always, do some research at Technet.com to find commands.
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