My experience has been much the same as Jeff's... I have flown a good number of my total hours in airplanes with heel brakes and I don't even think about where the brakes are... your feet move, the plane reacts, you mentally adjust without having to think about it. I don't notice much difference between the foot/ankle/knee/leg actions while working the brakes and rudder in aircraft with heel or toe brakes.
In the same way, I have flown about equal numbers of hours with throttle in right hand as in left and although I prefer stick in the right and throttle on the left, I don't have to think about which hand to advance in a touch & go. Your reflexes will pretty much figure out what to do in just about the amount of time that it takes you to taxi from the hangar to the runup area with a new control setup, so beyond that it's purely preference. Having said that, I do find that it requires a good deal more thought and attention to fly right seat in a side-by-side airplane! Not sure why; it must be the sight picture. Either that or my senses remind me that I'm not a CFI and I'm flying from the wrong seat ;o) Now to complicate matters just a bit, my Pietenpol steers with a rudder bar instead of pedals, and it has toe brakes. So you use your legs to steer the rudder bar (your heels shouldn't really be on the floor) but when you need brakes, you have to be pretty used to the brake pedals because the rudder bar may be making pretty wide swings at the same time that your toes need to be making very small motions with the brakes. As an example -and this happens to me because I fly an airplane that cruises at 65 or 70 MPH out of a big paved, controlled field with a main runway that is 8800' long by 150' wide- you land and see the next taxiway exit coming up and you hear "Experimental Four-One Charlie-Charlie, no delay exiting the runway" because you have a DC-6 air tanker with four R-2800 radials and almost 10,000 HP either coming down on final behind you or queued up at the hold line anxiously waiting to barrel out of there and go dump 3000 gallons of retardant on a fire. Still taxiing a little too fast as the yellow stripe sweeps away toward the taxiway, you have to swing clear of the active (push on that rudder bar pretty aggressively), keep the nose ahead of the tail (make rudder corrections with the rudder bar), and do some gentle braking (those toe brake pedals will be moving back and forth with respect to your feet and toes) till you pass the hold line to clear the active and start breathing again. But this is why we fly, eh? Oscar Zuniga Medford, OR