If this is for a mater of long feet, heel in towards back and toes angeled slightly out.
try using the shifter as it is intended. you will love it after a week or so of getting used to it.
Ok? Maybe I dont get your problem, if you have a heel toe shifter why do you want your toe under it?
Your HEEL does the UP shift by pressing down on it, and your TOE does the DOWN shift. Its a little weird to get used to but once you get it, its great. Most people have the stock heel toe shifter modded to get it closer to the board so you are not pulling your foot up so high.
My old Kawaski Police bike had the greatest system. Very close to the board, neutral between each gear (cop models only) and I could click the crap out of that tranny.
I have floor bds and the stock shifter on my TA. It can be adjusted by the control rod at each end.