It depends on the type of credit. I have 3 song credits and every time I buy an app it would ask me if I wanted to pay because I couldn't use the credits to pay for apps. This was a good thing because it gave me another safety net before money would actually change hands. There was a time when restoring apps meant "buying" them again and you wouldn't find out until after you "buy" them whether it was going to cost anything. Leaving these credits sitting in iTunes gave me a safety net so if I didn't get the "you already bought this would you like to download again?" I had another chance to back out. Happily things are better now and you can go to purchased items to redownload things rather than "buying" them again. If there is a type of store credit that can be used for apps, I'm not aware of it because the credits I had won't work for apps.
hope this helps...