we have this issue with our two at the moment, we dont use crates but they have a bed that would sleep a great dane!
they sleep in the kitchen and would scratch & scratch & scratch at the door until we let them in to sleep in the bedroom! Which, for want of a good nights sleep, we always gave into, but to be honest i got fed up cleaning another room in the house after them!!!
So about 6 weeks ago we started the 'bed' thing, when they would scratch we would get up and say 'bed' after a few false starts they got the message.
We are still learning but they now know that they have to stay in their beds until i get up in the morning, and then they can go in and have a cuddle with Daddy on the bed.
Its a learning curve, i mean we have Cava over a year and we are still learning with her. My most important piece of advice i can give is work as a team, theres no use you doing one thing and a partner doing another! poor dog will just get confused!
Best of luck & would love to see some pics soon!
owned by Cava a Tri Color, age 1 & Spud a Blenheim, age 8 months