My seed is set up in such a way that depending on where I want to go, I launch the boat from different locations. So I usually just carry it with me. Depending on the depth of the water where I would leave it, sometimes I break it down and put it in a chest just in case. The only time the boat is at "home" is when I'm returning from somewhere with metals, and it doesn't stay long. No real need for a harbor or boathouse. I also move bases so often that I usually don't need to take metals to the same place. I just move the benches and upgrades to the new spot.