try to get them out of the tree. chances are, the queen is still on the tree. if you don't get her, they will all end up back there. if you can cut the branch and then shake them off over the hive, or lay it on the hive, you'll have a better chance of not losing her.
don't put them in a super without frames. they will make a mess. swarms build a lot of comb, fast. they are in the shallow? feed them and see what happens. they will probably stay around :-)