Welcome Aboard! It's good to have another advocate "For the Boys!" I have a mixed age/breed bachelor flock of ten - all Nankin bantams with one lone Silkie. At the moment, they're split (6/4) into two sides of their bigger run while the three youngsters grow out fully. No Way was I putting little ones in directly with the top four ... they're a pushy little bunch, even on a good day! One of these days, I'll open the run back up and let them mingle, but not until I know they can hold their own. So far, so good!
For your new boys, if you can leave the extra coop and run where they can access it, if they need it, that would probably work. If they need it, it's there. If they don't, that's fine, too. In the very least, it will accustom them all to the structure so that, if you ever need to use it in the future, it's not a totally alien surprise for them.
Again, welcome to BYC. You've come to a good place!