I always seem to be confused about some aspect of cycling. Now is no exception. I have recently moved my seat position fairly far back at the insistence of what we can call my coach. Former racer, LBS owner, etc. Sure enough, my pedaling power increased, along with speeds, and virtually no hand, arm, or shoulder issues. Feels great. Now my confusion comes from whether I am using primarily quads or glutes in this position – and more importantly – what difference does it make which I am using? Also, from this back position, should I be using heals down or toes down as I come over the top? I will sleep much better if I eliminate the current confusion.

There is no right answer to this one. You must find what works for you. Move around, try new things, ride lots, keep what works.

Generally speaking the farther you move back the more you use your glutes and hamstrings. Also, the farther backwards you go on the saddle the more likely you are to slow down your pedal stroke and use power instead of speed in your pedal stroke, though there are always exceptions to the rule.

Where you end up depends on your body make up, strength and riding style.

My self, I prefer to be pretty far forward. I have huge quads and almost no glutes (always have been that way). I also have short legs and short femur length for my short legs. This for me means I need a fairly steep seat tube angle and need to be forward on the bike to maximize my strength.

Pro riders, or those considered to be very good riders tend to be longer legged, shorter bodied and tend to have somewhat more power in their glutes than quads, hence a more behind the bottom bracket approach.

It's really an individual thing and depends a lot on your body shape.

I always seem to be confused about some aspect of cycling. Now is no exception. I have recently moved my seat position fairly far back at the insistence of what we can call my coach. Former racer, LBS owner, etc. Sure enough, my pedaling power increased, along with speeds, and virtually no hand, arm, or shoulder issues. Feels great. Now my confusion comes from whether I am using primarily quads or glutes in this position – and more importantly – what difference does it make which I am using? Also, from this back position, should I be using heals down or toes down as I come over the top? I will sleep much better if I eliminate the current confusion.
Well, as you said, your power increased, speeds are faster, no issues with your upper body, and it feels great. What do you care?

If it feels right why mess with it?.......I think saddle position is arrived at by experimentation rather than a setting...

bboseley: Also, from this back position, should I be using heals down or toes down as I come over the top?

IMHO at the top you want heels down, poised for a strong push. At the bottom is where people have a personal preference for heel position. My preference is to generally have a neutral ankle position at the bottom of the stroke. In other words I don't force the heel down or point the toes down.