I finally decided to start a new thread since the old one had so many spin off.
The trainer and I have been playing phone tag, but I still wanted to update people on here.
As I mentioned, I bought a second crate yesterday. I set it up early and attached some water bowls to the door (very cool because the boy always tries to dump the water bowl and he can't dump this! -- before, we had resorted to a glass pie pan). I fed them in the crate, but I didn't put the food all the way back--I decided to go gradual as much as possible.
We were also having a problem that I hadn't mentioned with the girl. When going outside, she would go to the woodpile and burro into it and we couldn't get her out. She did this especially at night (I was thinking that she knew bedtime was looming). So I also bought harness style leashes and a tether with a stake for the ground. I only got 12 ft leashes because this isn't for all outdoor time--just when I need her to remain particularly close. We plan on using it for all potty time right now so that we KNOW that they went. Then, if they go we will detach them and play for a while. Except in the middle of the night.
Now, we get to bed time and I am honestly dreading it. We moved both crates into our room (we keep them with us as much as possible) while dh and I got ready for bed. We played with the dogs a bit--watched some more of those training videos from the clicker lady (finally getting dh to be more of an active participant so we can be on the same page). We had the dogs go potty and then we allowed them to get calm in our arms. When they seemed very sleepy we put them each in their own crate. The girl dog (previous crate hater) didn't whine or cry at all. The boy dog was mad though--he missed his sister. He gave it up after 5 min and went to sleep.
I took them out for pee at around 2:30. They peed and pooped (odd we normally don't have night poops--but I thought they were holding for a while because being tethered is new) and when I brought them in they both fought going in the crate but not as bad as before. I did have to move them to a new room so I could get some sleep, but they did calm faster than normal too.
All in all I think we are making progress. They are both napping right now in their crates (one per crate) and I didn't put them there. We just left the door open. This is good news to me because the girl had started to nap in a wedge between the couch and a table. I think she really likes her own space. I really think her brother was annoying her a lot.
And, though it may be too soon to tell, she is seeming happier in general and excited to be with all of us--even the kids. I still plan on working with the trainer, but I am really elated because these few simple changes are already making a big difference!