Canals and Submerged Structures.

I'm wanting to make a town based on canals instead of the usual road structure, I've messed with roads and towns, and I haven't got any results that I'm quite happy with yet, but I'm not sure how to do variable height assets (such as submerged structures, or structures that can go deep underground), and would like some help So it's my understanding of NBTs (I'll call them NBTs just so we're all on the same page), is that to make a structure that is both above ground and below ground, you would make an above ground NBT with a puzzle downwards, then an underground NBT with a puzzle facing upwards, but I'm not sure how to extrapolate this to a sky-facing submerged structure such as a canal basin. Any help, guides, anything would be lovingly appreciated, the only up to date stuff I've found is Conure's vids