just to clarify about the registry thing--it all depends which registry one deals with if a foal sired by a yearling can be registered or not. AMHA I believe has no rules regarding age, not for fillies or colts. AMHR on the other hand does not allow a foal to be registered if either of the parents were only a yearling at time of breeding. Ireland has its own registry does it not? So, you would need to find out if there are any age restrictions for breeding.
Time will tell if your colt got the job done. It's common for yearling colts to go through the motions if they get the chance, but many of those breedings do not result in conception. Of course about the time you figure that it won't happen because the colt is too young...that is when the mare will turn out to be in foal.
As for why it is a bad thing to breed with a yearling colt--the only real problem I see with it is it is bad for the colt's manners. The yearling that gets to breed a mare often hasn't had a lot of handling/mannering up to that point, and once he breeds he thinks he is really hot stuff, and manners (especially manners when the colt is out around other horses, say at a show) take second place to hormones. Of course you can overcome the lack of manners but it takes a little more effort than if the colt learns his manners well before he breeds.
There should be no additional problems with any pregnancy because the sire was only a yearling at time of conception. Now if it was a yearling filly that accidently got bred (by a yearling or otherwise) that would be a different matter. While there are cases where 2 year old fillies have delivered foals with no problems, if I had a yearling filly get bred, as long as I realized it early enough then I would have the pregnancy terminated.
As far as your question if your mares will have to be separated from the colt if they come into season again, I would say yes, because certainly he will be breeding them again next time around. Obviously if you have decided that you're okay with them being bred this year and you don't care if your yearling continues to breed them through each heat cycle, then you will leave him out with them. That is your choice.