I understand they get upset at being apart, but I really would separate them before you breed. Yes, you may want to wait until you notice them getting territorial, but what if you're not there and they injure each other? There is a very good chance of that. Or, what if they don't fight, but separating them causes them to become stressed and abort or abandon their kits? Unless you are going to research colony housing I would separate them now, wait until they get used to it, then breed them. It will avoid risks of a dead or injured pregnant doe.
Also, breed them separately for sure.
As for table breeding, I don't like it unless absolutely necessary. Does who don't mentally want to breed often have false pregnancies or small litters. They just don't do as good as if they bred willingly.
If your does are very nervous, there are lots ways to help. Feed a handful of spinach and/or put apple cider vinegar in the water for a week or so before breeding. I like to put an article of the buck's(like a hiding house, a toy, anything that smells like him) in the doe's cage overnight to get her used to his smell. That has helped my does a lot when they are being uncooperative. I also really like breeding in a neutral area. Just put the buck in the pen or large(unused) cage first for a little while(maybe 10 minutes) so he can spray and chin if he wants. Then, add the doe. If she is trying to hump him or bite him, push her away when she does it, but don't hold her down. If the buck starts breeding and she looks like she might bolt, sometimes I gently press her head or pet her head, but I don't force her.
Rabbits also like it if you breed in the morning or evening, and mine don't like overcast weather.
If they are still stubborn, try switching cages overnight, the buck in the doe cage and the doe in the buck cage. Then, in the morning, bring the buck back to his cage where the doe is waiting.