I have a pair of running shoes that fit, but the material on the heel area gave me awful blisters. What I did was Neosporin; bandage the site; and put duct tape on my heels and over the bandaids before putting on my workout shoes. After the workout, I just pulled the tape off and let the areas air out for a few hours before putting another bandage on.
If you use duct tape, I reccomend getting the really wide kind. I found that it stayed on better than the regular-sized duct tape. The regular dt works, but it tends to bunch up easier than the wider kind when the sweating begins.
And trust me, duct tape doesn't hurt to take off even with painful blisters.
Eventually, I acquired some moleskin and hotglued it into my running shoes. That solved the problem for good. You can also apply it to unbroken skin or stick it in the shoe, but I never could get it to stay put!! You can find moleskin at your local drugstore in the footcare section.
Another thing to try is to experiment with different types of lacing. A "Lace Lock" will help keep your heel from rubbing against the shoe.
http://www.fieggen.com/shoelace/locklacing.htm
I found that when my heels hurt, I would shift my feet forward in the shoe causing more blisters elsewhere. However if your shoe is snug or snugger, then it may make it more comfortable to have your heels in the correct position.
Anyhow, that is what has worked for me. YMMV.