So I have a converted kid trailer for cargo, but I am planning some camping trips via bike and wanted to bring my dogs. I was thinking of using a trailer frame with the plastic kennels bolted on to it to use for the dogs. One dog (boxer/coonhound mix, 65lbs) likes to run along side the bike on his lead, but the other (rat terrier, 20lbs) hates to. I was thinking that the bigger kennel bolted onto the trailer base with a smaller kennel bolted to the top of that would be a good solution for both dogs when they get tired and overnights. Has anyone done this before? How do you travel via bike with your dogs?

Don't your dogs get along well enough to be in the same trailer?
I haven't done it with a bike, but a neighbor used to drive all over with a 4-wheeler and 3 or 4 dogs in an open trailer behind it.

They do get along, but the big one is a puppy, and the smaller one is older. He is a bit more gentle and easy going. The coonhound mix won't stay in an open trailer. I'm more looking for a solution to when he needs a rest from running, and a place for the smaller dog during the trip.

You could try one big kennel, or a couple of smaller kennels.

But, I would experiment a bit with just the trailer first. Open the top with enclosed sides. Then get the big dog good and tired, and see if they would both stay together in the trailer.

The kids trailers are pretty small. I've built a custom cargo trailer a bit larger which is nice for bigger stuff (and would give more room for dogs, kennels, camping gear, etc.

We use the WIKE large 'Wagalong' trailer for our two jack russells (15lbs and 20lbs). It has a maximum weight capacity of 80lbs total. Here's a link to their site: Bike Trailer for Large Dog | Wike Bicycle Trailers - The Walk and Bike Company

I noticed they added a line of bicycles. This one was interesting ... Wike Box Bike | Wike Bicycle Trailers - The Walk and Bike Company

bikes at work bike trailers Bike Trailers | Bikes At Work can even be able to put them a meter/yard or so apart.