Which Quartus version to choose?

10.1 SP1 is the most recent release that should be very similar to what the kit documentation / reference designs are describing. 11.0 is a bit different in that the SOPC builder system is being somewhat deprecated for legacy uses and newer designs are encouraged to use the QSYS tool set instead. I believe you could still use legacy SOPC builder under version 11.0, but perhaps there will be some differences in the way you use the GUI and tools versus what the kit instructions / documentation show.

If you're feeling adventurous you should be able to get it to work with v11.0 possibly with some additional learning opportunities about the changes in quartus, but if you want the quickest simplest solution you certainly

could start with 10.1 SP1 or even earlier versions (10.0, 9.x) -- whatever was provided with the kit plus its later service packs.

On the other hand once you are familiar with the use of the kit under quartus, migrating your designs over

to v11.x and QSYS might be a good learning exercise, though perhaps not the very first thing you ought to

try as a beginner (I assume that soon 11.1 or 11.0 SP1 will take some of the rough edges off the newly introduced version 11.0's tools).