My LBS has a board for checking your arches, and they have special isoles for biking shoes. The soles come with various shims that allow you to adjust the fit of your shoes to you. A complete bike fit ($100 at me LBS) includes looking at how your shoes fit and helping you adjust your inserts and shims as needed to make sure that you are fitted properly.

Whatever you decide on, I can't recommend tri shoes enough. I love being able to ride my shoes without socks if I'm just doing a short evening ride or after I've been caught in a downpour and had my socks soaked through.