Well, from what I know there are two options.
One: IF you have X/Y and a 3ds or 2ds you can use pokebank to transfer them one box at a time to X or Y. Just note that they can't be transferred back down to B/W/B2/W2. Also pokebank costs $5 a year.
Two: You can trde them one by one to another B/W/B2/W2 game. This isn't as hard as it seems and you could probably get 2 boxes done in an hour if you are paying attention.
Source: My brain and this.
Hope this helps! Also congrats on the free Pokemon!