Congrats on your new puppy!
When we picked up Max, we had about the same length of drive. Hubby drove and I held Max in a blanket for the start of the trip. He got too hot (it was sunny in the passenger seat) so he ended up in the foot well by my feet, sleeping soundly under the a/c vents.
Wear a t-shirt for a few days and use that when you pick him up. Let him use it as a blanket. That way he can get used to your smell. Bring some water, a bowl for the water, a toy, some plastic bags. The breeder should be giving you some food, enough for a few days.
We let him eliminate before we started to drive home, then stopped off three times on the drive back. Time it for once every 1 1/2-2 hrs. Make sure he goes before getting back into the car. Try to limit the amount of water he gets, give him a little bit often, as opposed to a whole lot at once.
Usually they just end up settling down after a bit and sleeping.
I personally wouldn't use a crate. Especially if it's both of your picking up the pup. One can drive while the other can play, watch over, admire the new pup.
Most pups aren't used to the crate and 5-6hrs is a long time to keep him in there if you don't have to, especially since everything is new to him. Might be too stressful for the little guy.