The main difference between the download & boxed version is the extra contents which the box provides (like the Essential Instrument Collection) and naturally the fact that you also got a license for these extra's.
So; best way to continue from here is to first grab the latest Suite from the Ableton download page
. After you installed it simply add the livepacks from the CD's (eic2, session drums, etc.).
After that you'll end up with a full setup Suite.
In short; the CD's provide you with a basic version; then you can get extra updates from the Internet.