Yes, you'll be able to choose between either upgrade option or Custom (clean install).
To get the most benefit and experience fewer problems most all are recommending that you do a clean install. Your Windows 7 will run faster and better.
I know its a pain to do a clean install, with re-installing all your software, etc., but in the long run you won't regret. However, the choice is yours.
Just be sure all your drivers are up to date.