Keep them separate. That is the best way to go!
Rabbits ARE loners and like to be alone. (This is a true fact.)
Also, if you keep two or more rabbits in one cage, they will not be near as nice to you as if they are alone, so, just keep them separate.
~My opinion ~
Actually, no, not exactly. Rabbits are social animals, although they were bred to be stress resistant and good cage animals for about 200 years and will survive well enough alone they are still pretty close to their anchestors behaviour wise.
Here, it is even illegal to keep pet rabbits alone (well, a very questionable law, there are some others too that make things worse). Rather rare, imho, but some rabbits indeed are happier alone, had that case once in 7 years, girl got mobbed and depressed in company.
Although mine qualify as lifestock and not pets, I keep all 6 of them in pairs (my buck got a spayed girl as cuddlebun), because, well, when you see it, you'll know.
The thing is, the way most of us keep them doesn't really suit their instincts and social needs. It's a compromise.
Each of mine has a seperate hutch, two and two connected by a tunnel (my buck and his girl are my free range house bunnys, no cage). They always have the option to get out of each others sight, imho that's quite important.
But even then, characters need to be compatible, two Alphas together don't work. In nature, they just would part ways, they can't do that in captivity. I skipped that whole bonding thing by selecting a compatible companion from a litter, so mine are mother-daughter pairs.