Do you read to the younger children? Some parents let kids fall to sleep by watch some kid rated DVD while in their beds. Personally,I think they need to go to sleep without the family split on their minds.
Don't take this the wrong way, but maybe you could have prayer time first, then have bedtime stories or whatever to help them get their minds off of the problems with daddy....long enough that they can fall to sleep.
Praying for the parent who is not in the house is a very emotional thing for children, and especially if they see the LBP shed a tear or appear very sad. You have a heavy burden on you.
If daddy comes by to hug his children right at bedtime, seems like that would increase the emotional state for them. IDK, they are your kids...so you would know best about when he needs to come by. It doesn't help the kids' routine, and that's what you need to decide. They may need to adjust to having one parent with them when they go to bed.
It is not about what you feel should work in your M. It is about doing the work that gets the right results. Do what works!