Question) How do I apply these settings to a limited user account?
Answer) Change the account type to administrator, make the changes with LockDown My Computer, and change the account type back to limited when you're done.
Question) Do I have to be logged in to the account I want to configure, or can I do it from a different account?
Answer) You can configure a different account than the one logged in on by right-clicking the program icon, and selecting "Run As". It will ask you for a username and password. The program will run as if you were logged in under that account.
