First try limiting water intake right before bedtime. I would say no water 30 minutes before bed time. Take them out right before you go to bed for the night. If they wake you up in the night then take them out, if you wake them up to use the bathroom they will get used to that and never be able to sleep through the night. The puppies are about 9 weeks old now, correct? If so that is good with each passing week they will be able to hold it that much longer. If they continue to potty in the crate, take away the bedding so they have to lay it in, this will help them realize not to soil their sleeping area. It sounds mean but it is really the only way for them to learn not to soil their beds. (most dogs already know this and don't potty in the crate) Do they sleep together in same crate? If so you might need to seperate them until you get the potty in the crate issue under control( no need to punish both if it's just one that is not holding it).
Good luck, potty training is one of the hardest things to do but once they understand it's worth it.
oh, I agree about geting rid of the potty pads, I think it sends mixed messages as well.
Good luck.
Gina