It might be helpful to see a picture of your roosting area and your coop.
To make suggestions that might work. You can try to put them to bed under the nesting boxes every night for a couple of weeks and see if they start going there on their own and/or staying there until let out.
In my experience, some silkies do roost. However they don't fly so if you have high roosts they wouldn't be able to get up there without your physical help, or some sort of set up that allows them to climb up and down to their roost spots. (Assuming your current flock doesnt decide they like it). Again you can see if they'll stay there. But not all roost and may find the ground level more to thier liking.
I personally use pine shavings. As a lot of things can cause respitory issues with these little fluffies.
There's no way to say that a silkie would go and roost under your nesting boxes. As my silkies tend to sleep all over the coop, not in just one area, sometimes. Depending what's going on, like a broody, may mix it up or new flock members, etc.
Although the do often go under this roughly 45 degree angle piece of wood in the coop. So you may have some luck with them not getting pooped on with something like that.
You can try a few things, see what works, what doesn't and modify as you go to try to make it work.
How big is your flock? I hope some other flock owners with silkie additions stop in and give you suggestions for integrating. I only have silkies but they too can pick on new comers.
My thought is always slow intergration where they can see each other but not hurt eachother. With supervised time together daily, couple times, to break up fights and try to make it enjoyable. Like treats together, with several piles, to avoid pecking order issues.
From what I've read, it seems to me additions are often not old enough when added and the numbers are too small when adding silkies to already established flocks. Like adding two... I'm not saying this is the problem totally, but an observation.
Have you considered eggs and having one of your chickens hatch them out? This too may help silkies integrate better. Especially if they're hatched out by your top hen in the pecking order.
Just some ideas. Good luck, as I'm sure you will love your silkie additions! Hope your flock does too!!