Gavin-
For taking them home, I'd put them in the same carrier, I've plomped four little fluffballs into one before, because they were all soo attached! That was a short trip, though, but 2 in 1 would be fine for them, probably make them feel better. Plus, since I assume yours are littermates, they probably don't want to be too separated, it's enough being away from mommy.
As to confining them, each cat is different, so you really have to see what they're comfortable with. For the first night, definetly keep them in a small room where they won't feel lost. I have a big closet I usually use for this. After the first night, depending on whether or not they're hiding, let them explore a little, but carry them back to where the litterbox is at least every half hour, or they might have an accident. If, however, they spend their time hiding, I'd just sit in the little room with them for at least a few hours a day, until you feel that they're warming up to you. It's no fun chasing little kittens out from under the couch, across the room, and back under the couch again. If they're nervous, you want to introduce the rest of your house slowly, avioding rooms where there's lots of hiding places. Having to chase them out to check on them will make it harder for them to bond with you.
I've had them go both ways. Some are immediately "hey, just look at my new digs! I think I like this, oh a warm lap!", and others are "oh, no! I've been abducted by huge hairless aliens, and I'm quite sure they want to do experiments on me. I think I'll try to stay in the most inaccessable place possible, for, oh, a week?"
Best thing to do, is to go with your gut. They'll let you know what they're comfortable with, if you listen.
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