We're not crate fans either - although it was necessary for potty training. I think either blocking off a room or an expen is best for when you're gone. I gave Bailey a treat when she entered the expen - she always entered it cheerfully - so at least I didn't have to chase her around the house. After she gulped the treat, she wanted back out - lol. Bailey is a smart dog, I don't understand why she never caught on to this little trick? I guess, she didn't hate the expen!
It was our routine and she came to expect it.
As far as at night and in bed - yes, Bailey had the same issues. Her internal alarm clock is set at 4:30 - ours is set at 5:30. We taught her to lay back down until our alarm clock goes off. Just be stern and inflexible about this rule at all times. Inconsistency leads to confusion and bad behavior. That said, Bailey can't jump off our bed - so she's stuck with us.
Before Bailey slept with us, I kept her next to my side of the bed in a small gated off area - approx 3' x 4'. This is Bailey's room - complete with an ottoman converted into a bed, throw blanket, a stepping stool, pillows and miniature pic's on the wall - sooo cute!
These are my experiences - I hope they help you.
Good luck!