Hi Michelle, and Welcome to the Daily Puppy:
I think, as you said, that you do need to spend more time during the day allowing Doc to become more accustomed to his crate. In the meantime though, you don't wish to develop habits that are hard to break later.
If you can create a safe "corral" for Doc in your bedroom, that would be wonderful. Does Milo also sleep in your room? It might make Doc more comfortable if he is in the same area as Milo, but without Milo having the ability to interact with Doc.
Puppies will cry, (most of them) for the first 2 weeks or so that they are in their new home. It is hard, and heart wrenching so the closer the pup can be to you, the better. If nothing else, perhaps you can set it up so you can reach Doc from where you are sleeping just enough so he can lick your fingers and know you are there.
I think the whole process normally takes about 4 weeks before a routine becomes established. Sleep is highly overrated.
With Oliver, he was in my room and I would put him in his crate. I held him in my arms until he drifted off to sleep and then quietly put him in there. As soon as he woke, I would rush him downstairs and outside because an 8-9 week old puppy will need to relieve themselves every few hours. I would bring him back up to bed, cuddle him again until he fell asleep and put him back in his crate. After four weeks, he had it all figured out, and generally ended up sleeping with me. Epic fail, sort of!
However, having said that, his crate is still his safe place that he enjoys. Oliver is 8 years old now, and if we travel, as long as he has his crate, he's happy.
Henry was a little more difficult as he contracted Giardia so he had no control over his bowels at all. I honestly think winter is easier for housetraining/crate training than summer as the cold air makes them "go" immediately and the parasites are long gone from the frost and snow.
You sound like you have a good deal of common sense, so work out whatever works for you. It seems like a long time when you're living through this phase, but ultimately looking back, it's but a mere blip on the highway of life.
You are also laying a terrific foundation for your dog(s). I noticed both of them in the Recently Added Section, but didn't have time to comment. They are lovely.
Good luck, and do keep us posted! Amongst us all, we're bound to find a solution.
Deborah, Oliver & Henry's Mum