You can perform a jump in version. You can get all the changed files that go from beta to beta on Infopop's support forums.
You shouldn't have any problems upgrading, I know I have walked several people on this board through the installation and upgrades and we haven't ran into a problem yet.
What you should do is, make a backup copy of your cgi-bin and Templates folder before installing the updates, that way you can restore them if you run into problems.

Just a suggestion.
The final is great, I haven't seen any problems with it. Wish you luck with your upgrades. The latest release to date to my knowledge is 6.01 GOLD? Is that right guys, I haven't checked infopop today.