I would say if penning them together is really important to you; get him in proper condition, and then just turn them all out together to figure things out...they WILL eventually, and as mentioned, you could rug him to prevent bad nip marks. It could take a couple of weeks, or it may take a matter of days for them to work out the new heirarchy. Just make sure there are a few more piles of hay than there are horses, and make sure they are spread out as far as you can manage, so each horse gets his share.
Something that one of the barns I frequented alot, did, was to put lower members of the herd out into the field first in the mornings, with the hay, and then bring the more dominant ones out. That seemed to go so much smoother than putting the lower members in last...not sure why, but it just did; I've found the same thing with my own horses, when bringing in a new one...if I turn out the new one first (after the initial fence type meet and greet, and quarentine), it just seems to go better...
That said, unless you really don't want to have to feed separately for the long hual, you probably have the best situation right now, as it is; horses in pairs that get along. Especially because most places now a days don't have alot of space for horses to really dork around when integrating new members, it really is safer for the horses, to make sure they are in with horses they can get along with.
At the place I board my mare, she was in with a couple of geldings for a while...and then out of no where she started coming up with some nasty bite marks, so I had the BO separate them back out again; it's not the largest place, for horses to be idiots toward each other, so it's best if they are in their own paddocks. If the arrangement you have works right now, I would say keep it...they would eventually figure things out between each other, but if you don't have to go through all that (and potentially have them injure each other pretty good)? I'd say to not go through it.
"The ideal horseman has the courage of a lion, the patience of a saint, and the hands of a woman..."