I don't know if I can help, but I would like a bit more info. Have you trained him to go potty outside or inside on pee pads? What time of night does he poop on your bed? (or best guess). Are you gone during the day (at work or otherwise)?
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crate training doesn't really work on him, because he will pee and poo in his crate.
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but now he's gotten into the habit where he poo's in my bed when we sleep at night.
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I am not a behaviorialist, but I would guess these 2 issues are related. Somewhere along the line, he has accustomed himself to deficating and voiding in his "den".
I mean if you are serious about breaking this bad habit, I would set my alarm clock to around 3 or 4 am, get up and take him out for a bathroom break. You may have to do this for up to a month or longer, for it to become his habit. (You may have to adjust the timing as you determine when he is actually releiving himself). What you are doing is training him to get up and go potty elsewhere and not on the bed. If you decide to keep him in the crate until he learns this behavior, you will still need to do the same thing so that he learns that he poops and pees somewhere else other than the crate.
My other best recommendation is to take him outside to do his business. (if you are not already doing this). When he learns that there is no place in the house that is acceptable to do his business, he will soon learn that the entire house is the "den" and the outside is where business is taken care of.
Just my opinion. But it will take some committment and work on your part. (almost like re-training him - starting from square 1). But you will have a much better relationship with him. You may have to consider x-pening him and limiting his run of the house to only certain rooms or his x-pen until he learns where to go.