You want her separate during the incubation so she isn't disturbed by other hens kicking eggs around and laying more in the nest. If your coop is big enough, put the crate in there, so she isn't far away from all the other birds, that way they can hear the chicks in the eggs hatching. After they are a week old, and eating well, you could try letting mom and babies in with the rest.
If your rooster is a silkie he is unlikely to hurt babies. I find other jealous silkie hens can be a problem because they try and adopt the little ones away from mom, and sometimes babies can be caught between fighting hens. That's why I keep the babies a little apart for about the first week and then see how it goes from there.
I'm sure a lot depends on your birds personalities which you know best. Good Luck with your hatch.