My question is this:
   Does IQ only improve due to practice time devoted to each system?  Or is it affected by the use of that particular set in actual games as well???

I took over a team that had been running the press and want to make a change to either man or zone.  I've got 30-33 minutes to spend on whichever defense I choose.  In the transition phase however, is it best to stick with the press until the other IQ steps up a bit, play a combo halfcourt/MTM(or zone), or just go all out MTM (or zone) with weak IQs?

I would stick with the defense that you have better iq's in until the iq's for the new defense catch up.

IQ either improves only due to practice time, or if PT is a factor, it's incredibly small. 

Depends what sort of season you think your team is capable of. If there's not a lot coming back, the ratings are down, you have a lot of freshmen, etc. then I'd say to being the transition and throw your minutes into building the team you want for the future. If you've got a solid core and 20+ wins and/or a tournament appearance looks possible, then you might be better off to devote a chunk of that time to the press and running it this season (preserving/improving your school presitge will go a long way toward recruiting)  while putting a mild number of minutes in the defense you want to run in the future so that the IQ's start to improve there as well.