I hate to tell you this but, you are going to want to enter your inventory the old fashioned way. Why? Because you will find half of the stuff you sell different, plus many states require unique bar codes, PLUS, your scanner may or may not scan the check digits, PLUS the list goes on and on.
I know it may seem daunting, but it is worth it to take a day or two and enter all of your inventory MANUALLY (sucks, i know).
Best way I have seen is to have two people working together, one a runner and counter and the other doing the scanning and data entry.