Bobert- Below are three links with varying kinds of bat removal information for your general area. Seems to me you'll want to know what kind of bats you have, and whether there are babies. Beyond that you may find it's worth it to hire an experienced and effective bat removal company to reduce your exposure to the disease dangers while protecting the bats from unnecessary stress.

I'd at least spread plastic over the stored goods in the meantime. One of the links gives advice regarding the kind of protective measures to take when handling cleanup- you may need to first decide how to remove the guano that has already dropped on your boxes- be careful!

http://www.batmanagement.com/Ordering/eviction%20package/evictpack.html

http://www.wildlife-removal.com/bat.htm

http://www.probatremoval.com/northcarolinabatremoval.htm