I wear orthotics in my running shoes, which works great.
Technically, I'm also supposed to wear a lift at all times in my left shoe only.... according to the PT, I have a leg length discrepancy, so the lift is intended to even things out. I did obediently wear the lift for about a year - and they didn't really fit in anything but a few pairs of clunky, fugly loafers. Definetly didn't work for sandals or high heels.
I got fed up with that, and did some research about leg length discrepancies. I found out that they can be acquired or congenital. I wasn't sure mine was truly congenital. I ended up taking up yoga, and after awhile of consistent daily practice and lots of downward dog's, the discrepancy completely disappeared! Not only that, but the bunion on my longer leg decreased in size.
If I don't keep up with the yoga, the discrepancy comes right back, along with the bunion, and other aches and pains in my back, etc. Another clue is that my one pant leg starts to drag on the ground. So I am now pretty certain my discrepancy is acquired and not congenital.
I don't know if that answered your question or not - your issue could be entirely different. I'll add that I am judicious with my use of high heels. I wear flats more often and even with flats I rotate frequently.
There are a lot of people on YLF with fussy feet and it seems most of us are able to find fashionable shoes that baby our feet and don't make matters worse.
Last thought: if you are a runner, your feet probably swell a lot, after running. I have discovered it helps to buy wider widths or go up a 1/2 size to accomodate for that.