also why does he only want on the bed or couch when it thunders

He wants on the bed when it thunders because he is scairt. Dogs are afraid of thunder. We had a border collie who was never, not ever allowed in the house, but my dad would relent during thunder storms and allow the dog to creep into the closet and hide under the clothes.
You might make your dog a bed in the closet. The clothes muffled the noise but if the previous owner allowed the dog on the bed, good luck telling him "no" now.
Dogs are very persistent. I would bet you are going to make room and let him cuddle up under the covers with you in the end :)

I have two thunder shy dogs. Actually, they both begin to tense when the barometer starts down.

I have worked with them by doing fun things when they become agitated. Toy play, Speaking happily and laughing when thunder booms. Took months, but they began to feel my lack of agitation and how calm I was---and they became slowly less agitated.

Make him a bed beside yours. Molly(our female rescue) was more calm in a wire kennel beside our bed---with an old sleeping bag on the top to make a cave. We just left the door open. She still uses that 'cave' on occasion.

Ignore his unwanted behavior. If he shivers in fear, get toys out. Do fun things, speak happily--(be happy, they pick up on that). Scratch where ever they like scratching.

Do NOT feel sorry for them---or allow that emotion to exist. By not allowing unwanted behavior, you make them practice wanted behavior---which makes them a much happier, more balanced dog.

Great advice re: the thunder, but can you explain how he 'freaks out' at night.......with no thunder?
If he's just wanting in the bed with you I'd set up a crate, as handymac described, so that he can still be close to you, yet not in your bed. You might also try using night lights throughout the house and maybe leave a radio/tv on low in another part of the house. Is it possible he's hearing noises outside, or inside, the house?
How long have you had him?

Your dog knows that your bed is very comfortable that he wants to sleep beside you. You can try to place his bed up on an elevated surface so he can see you. At least you can be able to reach out and touch him, but his bed should be far enough that he can't make the leap onto your covers.
Make bedtime a routine for your dog. Reward him with a nighttime treat, like a special toy he only gets when he goes to bed.