Put them inside & turn off the lights, assuming that you have them. Gently lift each one onto the perch, tell them it's time for all good chickens to go to sleep & let them do that chicken cuddle thing to get and stay warm. You may be able to towel dry them or even blow dry them if they're really soaking wet, as suggested above.
At some point, there are a couple of things that will need to happen: 1) they're going to need to come in out of the inclement weather; 2) they're going to have to find their pecking order; & 3) they're going to need to learn that at some point it's bedtime for Bonzo.
I agree with covering the rest of the run if possible. Fall rains & Winter snow & cold will be upon us all sooner than we might like.
And if they're stirring up trouble amongst themselves when inside, may I ask how many birds do you have & how large is their house? It could be that they don't have enough space, it could be that you have a couple of very saucy birds making trouble for everyone else, it could be that they are jockeying for position in the flock, it could be some, all or none of the above. And who's causing trouble...hens, roos, everyone?