Dumb question about cleats.
 

Does it make a huge difference which set of holes I put my cleats on on my shoes. I mean... will it make a difference in what muscles are being used more? The closer to the front of the foot the more of my calves I'll be using right?

Well if they are not positioned correctly it can lead to lots of uneccesary pain and injury. Very generally speaking the spindle of your pedal wants to be centered on the ball of your foot. Personal preference would be incremental forward or back from this position.

+1... if they're not positioned correctly, you can get hot spots too, in addition to knee aches/pains.

Oh crap. The ball of the foot is..... right in the middle of the widest part of the frontal half of the foot correct?

I'm glad I asked this. Didn't know the position mattered.

Take your shoes off, stand up, and now lift your heels off the floor. The part that all your weight is on is the balls of your feet. Enjoy--

[edit] -- calves are a more-or-less a stabilizing muscle in the pedal stroke (yes, we could discuss ankling, but let's get past decent fit first, shall we?). You want to use the large muscles of your legs: butt, guads, hamstrings...

I'm having trouble getting the cleats in a comfortable position, but I understand the idea. Thanks.

Getting cleats to a comfortable position is a PITA. Just keep adjusting them until you feel comfortable. Try to get the cleats in a position so that when you're riding, your foot is in the same position it would be if you were riding w/o clipless.