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My SQ bunch didn't understand the concept of getting out of the rain either, so I had to top part of the run. Silkies you have to be careful with them, because when it gets cold and it rains - their feathers soak up water and don't shed it like regular feathers would...So they can get wet to the skin or "soaked to the bone" as the saying goes....
So if it turns cold too soon, and they aren't dried out, they can catch a chill and its known to kill silkies.
I would suggest topping or tarping your run, or make a bigger building for them, and just leave them in the building on rainy days, and don't allow them out in the rain in cooler months - hot/warm months it wouldn't be an issue at all though. Many people who breed and raise silkies especially the Show quality birds keep them indoors in breeding cages/pens, or their whole set up is roofed so they can't get rained on.
as for teaching them how to go up, with new birds I just have to put them in a few days, and put them in front of the door and give them a boost to the butt, they go in on their own the past foot...they learn that the coop is the place to go up at night. Does your building happen to have a ramp to get up into it, or is it on the ground? Some silkies just don't take to ramps well at all, you'll either need to make it really long so there isn't much incline at all and they can feel secure, or if possible lower the building or entrance to be on the ground or only a couple inches off the ground.
it is on the ground we converted a storage shed into a coop so there is no ramp. i hatched these from eggs of show quality chickens i hope i have a few we can show. i had them in the coop for about 3 weeks so they will learn where their home is and where they sleep but they just do not seem to know that they live in there. rain gets in a little but only if the wind is blowing really hard a little gets in thru the window that is covere in chicken wire and thru the door a little not enough to make it muddy just a light mist gets in but my husband if it stops raining long enough this weekend he is going to fix that. i just hate seeing them like that and i guess for the rest of hte winter i will keep them inside the coop at all times because it has been raining here constintly for weeks and i will not be able to close the top of the run so that rain does not get in till after christmas. maybe i can but a small tarp in the cornor they seem to like for now but that will not last long but at least they will be able to be out for a little while. guess i need to think about building a diggerent coop and run for them but with money really tight it would be a while before i could do that.