How do some of you guys differentiate the two? Put the better rebounder at C, or the better scorer at PF? Should the guy with better BH or ATH be at PF instead of C?

Take a peak at my Johnson C. Smith squad, my two best players (Mixon and Lane) are both bigs listed at center, but I put Mixon at C and Lane at PF for my exhibition games. Mixon is my best scorer, is it to my best advantage to put him at C? Will he get more or less scoring chances at C than PF, or does it not matter so much?

For me, it depends on the match-ups on offense and defense.
Most of the time, these guy are inter-changeable (for man to man defense).  Usually if I have a guy who is hella slow, I would probably put him at C where most likely the other slowest guy would be on the other team.  Obviously for both you would need the right ratings for them (REB, LP, ATH).
Since you are playing a zone, I don't think it matters.
For offense, as long as you give the right distribution, it won't matter if they are at PF or C.

Well ... I would normally play the guy who is better P, BH, PE at the PF spot and the one who is better at LP. REB, BLK at the C spot.  If playing M2M defense, I will shift them around to better matchup with the other team's offensive threats.

for most games I'd put Lane at C and Mixon at PF, the ever-so-slight ATH/SPD combo would play better at PF, and the slight boost on BH/P is more useful at PF, too. It may be statistically insignificant to others who have played many more games than me, but that's what I'd do. Like the others said, play matchups, too, you might have to use Mixon's D/BLK to help shut down an opposing big, and you might use his LP to exploit an inferior defender at PF. So don't be afraid to mix and match every game.

id put mixon at PF for most of the year due to the higher BH and speed... but it also depends on matchups...

I agree they are interchangeable especially for a M2M defense to expose matchups.

When I first started playing I was told to put your better BH at PF and your better P at Center.  I wouldn't let it be the only determining factor but also something to consider as Centers do wind up needing to pass from down low more and PF do tend to move with the ball.