Aww you have beautiful bunnies!
Your setup is the same as ours by the sound of it. When we had our girls spayed, we kept them indoors for a full fortnight to allow them to heal, on vet advice. The first 5 days they were in a large puppy pen and we only let them out after about day 3 to stretch their legs really, poor things! Then they were allowed to poke about the utility room for the remaining time, but never allowed to stretch or climb anything. Once the fortnight was up, they were allowed to go back outside into their shed, where their 2-storey hutch was also housed. They healed beautifully, no problems at all.
We never separated ours - they're bonded sisters - and our vet never suggested they be separated either. In fact, we have never separated them; if one needs the vet, they both go. Always have, always will. They will only ever be separated upon first death. It's not worth the risk to separate them beforehand, even for quick vet visits, because if they come back smelling differently there is a chance that the other rabbit will reject them and their bond could be broken.
Don't be alarmed when your girls come back after being spayed and are super-dopey and do nothing but sleep. It's normal - they've just had major surgery and will still be off their faces on the anaesthetic. They probably won't eat properly either, ours didn't. Offer them water, i.e. take it to them as they may not feel like moving much. And food, for the same reason, although don't be worried if they refuse it. They will lick their wounds, it's normal. Pop them on towels, or vet bed, rather than hay or straw, as fleece is softer for them to lie on. They will pee/poop on it though.
Don't over-fuss them either when they come home. Just partially cover the puppy pen so they can snooze and settle, keep an eye on them (obviously), but just leave them to get over their trauma. In 48hrs you can fuss as much as you like as they should be back to normal - wide awake, eating, drinking, etc. And it's great to have them in the house for a bit!
