What can I do now that it’s cold to get them back in the coop?
		
		
	 
So this is your first question.  How can you get the three chickens to sleep in their coop instead of in the run?  Go out every night and lock them in the coop.  Once it is dark it should be easy to catch them.  And I'd take down that roost in the run.  You need to be consistent and do this every night until they get the message.  I've had some catch on in a day or two.  I've had some it took over two weeks.  Be consistent, they will eventually get the message.
Some people put them on the roosts, I just toss them in and lock the door.  They will survive either way.
	
		
	
	
		
		
			I also have 3 more hens which are about 37 weeks and one rooster who is also about 27 weeks old in another coop. I have tried integrating them about 5 times already and have to separate them again.
		
		
	 
What have you done to try to integrate them?  What has the procedure been?  What did the results like?  Why did you feel you needed to separate them?  
I assume they have been housed across wire so they can see each other for a while.  How long?  They are all old enough so it's not like integrating chicks with adults.  What I'd expect to happen is that they will decide on the pecking order and integration is over.  Sometimes that is extremely smooth but it sometimes involves some fighting.  Quite often it involves running away and chasing.  As long as the weaker can run away and get away it usually ends with no one hurt.  If it cannot, the winner doesn't know it won so it keeps attacking.  That's a good example of why I don't believe in magic numbers for how many square feet per chicken you need.  How far can a chicken run in a 7' x 10' run, especially if they start in the middle?  
You can greatly improve the quality of what room you have by adding "clutter".  Clutter means something they can hide under, behind, or over.  Something to break the line of sight.  Maybe put a satellite dish or pallet up on blocks or lean a piece of plywood against the fence (fastened so the wind can't blow it over).  Some people put a table in there so they can get on top or use a perch high enough the others can't peck their feet from the ground.  
As long as no one is getting injured I tend to let them fight it out but I have a lot of room.  The tighter they are the more risky this is but they do have to decide on a pecking order.
Without knowing exactly what you have tried before I'd try opening the door between the two runs and let them sleep separately until they have proven that they can peacefully coexist in those runs for at least a week.  Then at night I'd lock the young ones in the main coop after dark and lock up their small coop to stay locked up so they can't go back to it the following night..  Then be down there first thing as they are waking up to see how it is going.  Make further decisions based on what you see.  
More room would make it easier but you can probably manage.  Good luck!