There are many variables to your question. Are your hives mature or are they package bees or NUCs?
The hive with the queen most attractive to the bees will have bees drift to her hive. It happens most often with package bees but drifting is always a possibility. With packages, set them a bit farther away from each other than their permanent location. When they are established, you can move them a foot or two (up to three feet) per day to their final location. That should minimize drifting.
If you observe one hive growing faster than the other, (or, maybe the bees are drifting), you can switch the hives to equalize the populations. Foragers will return to their original location, even if you switch/move their hive. If you choose that option, you don't need to separate the hives at the beginning. When I say "switch" the hives, I mean to take hive number one and place it where hive number two was and visa versa. HTH
P.S. I set my hives on a bench and leave enough space between hives to set the top cover between them during inspections. It gives me a clean, convenient place to stack the supers during inspections.