In DIII I've got a 6'6" PF with low speed and a 6'8" C with better speed.  The C's rebounding and block stats are better but not by a ton. They both have good LP and decent Perimiter ratings.  I'm wondering if I'd be better off switching them up so that my PF plays C and vice versa, but am not sure how much size will affect things or if I should just keep them where they're at.  Any help would be appreciated.

Center:
http://whatifsports.com/hd/PlayerProfile/Ratings.aspx?tid=0&pid=2195761

PF:
http://whatifsports.com/hd/PlayerProfile/Ratings.aspx?tid=0&pid=2195760

I guess I should add that I run a flex offense and zone D

I don't know if there is a huge difference in those two guys but you are probably better off putting the higher rebounding guy at C.  

Height and weight don't matter, nor do listed positions - just window dressing. The only things that matter are ratings and IQs.

Backboy is 100% correct. Height is a non-factor. A player's skills for the position is all that matters. You can ignore player position labels too. The ratings for each skill are what determine his ability in that area. A 6'4" player with a 75 Rebounding rating will be better than a 6'10" player with a 60 Rebounding rating. A few seasons ago, I had a PF starting at PG and a Center as my backup SG because they had the best skills for those positions.

Cool.  Thanks guys.