Put them in the pen at night when they are all roosting, the transition seems to go smoother that way, don't put the new chickens in with your existing flock for a few weeks though. Always isolate new birds you bring in to make sure they don;t have any disease that could be passed toy our flock.
Also, you might want to consider going through the "chick phase" again to ensure you get healthy chickens. (Order hatching eggs or from a hatchery.) OR get them from a reputable breeder- healthy chicks.
There are many diseases that are invisible- they can be carriers and pass your quarantine. Then get your other birds sick.
Don't let anyone bully your silkies. They have a soft spot like a baby on top of their heads. Their skulls have a hole in them. They can die from a single peck on the head in the right place or become brain damaged. Many people mix their silkies in with the rest of the flock- and have no problems. My silkies were near the top of the pecking order before I separated them into their own flock (because I have 11 of them and wanted them to be separate).
Just make sure they are not bullied and hurt by larger chickens.
Congratulations on your getting silkies soon! Silkies are really different and sweet. I love how the roosters get along (well after they establish the pecking order that is). They are fluffy and snuggly. Here is a tutorial on how to bathe them if they need it:
How do you separate/quarantine new chickens if you only have one coop and one run? I've heard that you have to do that for at least 4 weeks. Where could you possibly keep them for that long? Or are you supposed to have a 2nd coop and run just for this?