Stomper (funny name for a little yorkie huh?!) sleeps in his crate at night. He is now 12 weeks old. We get up once at 4:30 AM to let him go pottie on the pads. We don't let Stomper eat or drink after 7 PM and always feed him at the same time every day. This helps us monitor when he will go pottie - he pee all day long, but goes poop no more than 3 times. Give that a try...it might help! Make sure you are not giving your puppy too much food. It is not normal for them to pottie on their beds, so he might be eating too much food.
Good luck!