I think i'm understanding you correctly, and the answer to your question is a tentative "yes", but it depends totally on how well the software has been written (and where it stores it's data). If it recognises applications on a "per user" basis then you should be fine, but if it is badly written and only recognises the computer on a "per computer" basis then it might be putting the data in a location that's shared between all logged-on users.
Anyway, adding a new user is a non-destructive process, so the easiest way for you to confirm this is to try it.