I traveled the rivers from Chicago to Kentucky last fall with my 60 lb. dog Pogo. We often had to anchor
rather than go to shore and Pogo learned to go on a piece of carpet secured to the bow. He pees in the scuppers.
It was a hard first two days while poor Pogo had to figure out what to do. I "walked" him to the bow with leash and plastic pick up bag. Tried everything I could think of. But it still took a couple of days and once he peed in the very back of the pilot berth. But once he went in the right place, all the stress went out of him. He was a relaxed dog, knowing any time he needed to go he could. Now we cruise together without worry.
I wish you well on your travels.
My one worry for the ICW is if your dog likes to swim to watch out in areas that have alligators.