The GMATPrep software you get from the CD or from the website should be exactly the same. It's highly likely you'll see overlap!

No harm in doing GMATPrep more than once, even if you may see repeats. It's a fairly big database of questions, and since it's computer adaptive, if you improve, you'll see harder (and therefore new) questions. You might also consider, at the end of your prep, GMATFocus, though some people find it expensive for what you get. GMATFocus is an official GMAC product and also consists of real (retired) GMAT questions, so is a lot like GMATPrep. It's computer adaptive, so most questions will be at your ability level, and gives you a reasonably accurate score at the end. It is, however, $25 for 24 questions, and you can only take each test once. I like it, but some people really do not, so I'd suggest reading other reviews before purchase.