I just take them from the Mom, put them in "whatever I have handy... a small box, bag etc.," then put them in the freezer. After they are frozen, I put them in a freezer Zip-lock bag with the rest of the pinkies. I have a vacuum sealer, but used it for the mice and rats since they aren't in the freezer very long before becoming snake food.
Most of my Mommy mice are pretty nice after giving birth and don't get very protective when I get near the nest. I had one that would try to bite, though. I started giving them a treat when I wanted to look at the babies or take some for snake food. That's worked great for me. I just give them a Cheerio or piece of my dog's mini chunk dog food. They love it and are more interested in eating their snack than in worrying about me. Sounds like you'll enjoy raising mice for your "soon-to-be" new snake. Congrats in advance and have fun. If you have any other questions, don't hesitate to ask. I'm sure someone here will be able to help you out.