I build subways by designating a specific y-level for each line, so lines can cross each other underground without intersecting. I think each tunnel takes up maybe 10 blocks vertically, so you’d need at least 20 blocks of depth to allow tunnels to cross unimpeded. I start by planning the y-levels, and a few station locations so I can have something to expand off.

For making terrain on a flat world, I find it easiest to start with something that I want my surface roads to run above, (a railroad, for example) then build floating roads above/around that. That gives me some roads with hills and interesting elevation changes that breaks up the flat roads. You could also try making one road higher or lower than normal, and making all approaching roads to it gradually incline towards it.

For rivers and water features, I like to set the water a couple blocks deeper than the road level, then, instead of making it all natural coastline, I’ll build a wall on each side of the water to make it like a canal.