I think any version of ProTracker should work with all Amigas. At least all running Workbench 2 or newer as the Amiga's audio capabilities haven't changed since the first Amiga was released. So the newest version you can find I suppose. Anyone else know any different?
ProTracker is definitely quite hard to begin with. You have to remember that it developed from a programmers point of view more than a musicians which goes some way to explain the interface and why it works as it does. I would recommend you give OctaMED Pro a try instead as you should be more at home with that as it is designed more with a musician in mind.