How do I change player setting so my position players only play a few innings each game?  I understand how to limit pitch counts for pitches but I cannot figure out how to have the sim make multiple substitutions during spring training.

Change the defensive and rest settings under Manager Settings. 

Or play him a full game then rest him two games...achieve's the same thing.

This is what I use for spring training:

Defensive replacements: winning by 1 or more runs in 7th inning or later
Player rest: winning by 1 or more runs in the 5th inning or later
Player rest: losing by 1 or more runs in the 5th inning or later

don;t forget to change them back to your normal settings for the regular season once spring training concludes.

I also set all requirements to the lowest amount of runs (1) and the earliest inning like tec to get guys coming into the game early.  I also set things like double switch and pinch hitting to very aggressive so that they happen more.  Then I monitor the players and try to get every guy 27-30 AB's