Don't underestimate the power of your shoe laces! Not only the type (more elastic, thicker, tubular, etc.) but the style of lacing of your shoes can help to augment the fit of your shoes and also be used to reduce irritation to some parts of your foot (called gap lacing).
When it comes to shoe lacing, it isn't something that we think much about - it's old hat how we put those laces through the eyelits on a new pair of shoes (usually called 'criss cross' lacing). A few changes to your lacing can help your foot feel more secure in a shoe when you have a narrow heel but a wider forefoot. If you have a prominence on the top of your foot, skipping over a few areas to take pressure off can reduce irritation.
There is a great website that demonstrates more types of lacing than you ever thought could possibly exist and this site even spells out the pro's and con's of each lacing type. Check it out here, it's definitely worth perusing! For running shoe lacing techniques by problem, check out this runner's blog.