It only updates the necessary files - in other words it's a selective patching process - however if you're installing from a retail disc and then using the GameStop app to update them, you may first need to detect the installation.  Use Detect Application on the Options (gear thingy) drop-down menu..

If you prefer to use the new Stardock Central application instead, I think I remember reading that you can contact support@stardock.com about getting your keys changed over - since you registered it with Stardock in the first place.  But aside from a few teething problems with the 2.04 update that I think are ironed out or at least there are known workarounds for, the other one will do fine.