It might be best to put them in the same area, each with their own large pens. Like, no free roaming. One bun might feel punished being caged when not used to it, or even might be too distracted trying to escape the cage that they wont try to mark. Likewise, they wont really be forced to see one another while on opposite sides of the house, so trying to get any prebonding by swapping this way isnt going to really do anything. Prebonding works best if each is penned/caged where they have to see one another and smell one another.
I reccomend getting two pens and setting them up next to one another. Keep their pens about 10 inches apart. This way they can see and smell one another (get used to one another) but cannot fight. Like this, they will know there is another bunny, and they will see the bunny is harmless to them. Youll do this for a few weeks so that they each get used to their new space.
After a few weeks of them set up next to one another, you begin swapping their pens. Bun1 goes into pen2 and Bun2 goes into pen1. Youll swap like this once a day for atleast a month. Doing this doesnt change their hierarchy. Theres always going to be a “top bun” and a “bottom bun”. Dominant bun will be the top bun, and submissive bun will be the bottom bun. A healthy bunny bond has these statuses. Swapping like this aids in the bonding process. Theyll be getting used to eachothers smells in “their” territory. Swapping them basically teaches them how to share
When you start bonding sessions, expect a bit of aggression. Always stop the aggression and redirect to something positive. If one bunny chases the other, stop the chasing, squish them comfortably together, and pet them. Mounting is acceptable during bonding. Nipping is also acceptable as its how rabbits say “I dont like what youre doing”. Chasing, biting, lunging, boxing, ect should all be stopped, though. The more rabbits fight, the less likely they will bond. If you follow through with the prebonding (cages next to one another for a few weeks, then swapping for atleast a month), theyll be more likely to bond as theyre already used to having one another around and in their personal space.