I don't really have any suggestions for footware. I use whatever I have to wear for the gig. Sometimes tennis shoes, sometimes dress shoes, sometimes it's my Capezio jazz dance shoe which has little to no sole. I know guys that prefer to wear their cowboy or Doc Martens boots when them play!
My Kick pedal technique varies depending on what I play or need to express on the drum. Playing heel down or flat-footed is one of the ways that I play. Personally, I don't use this technique when I need a lot of speed or volume, but there are plenty of drummers, Doanne Perry comes to mind, who play "flat-footed" with no problem. Whether it's single or double Kick pedals, single or double Kick drums, there are those who play it all, high and low volume, using the heel down
If I were you, I would develop other techniques to use and have at your disposal. Learn to play with the heel up too. Learn to use your leg (ie. leg thrust) with the heel up as well. Doing so will give you more to work with, or at the very least more choices as to how you'll achieve the sound you need at a given moment.
If you haven't done so, read my article entitled http://www.drummercafe.com/content/view/11/28/
]Kick Pedal Technique
. You might be able to glean a few things from that ... giving you more insight as to what direction you need to take.
If you warm-up properly and stretch out, you shouldn't run into any problems. You may find a shoe that will assist you to stay more relaxed and position your foot in a better place for what you
need. I prefer to have my foot as close to the pedal board as possible, so thick soles aren't for me. Many others feel the same way, which is why they've gone the extreme by playing without shoes ... even playing barefoot.
Hope this helps.