On my map Correlation [previously known as Atrophy], I'm stumped. I merged the bases a single wall's width underneath the ground, and I don't know how to continue the base up to the second floor, while still being smooth and able to mix with everything else that is not merged [the bases are one wall's width below a normal Block, Large]. I'd love ideas to make the bases normal-ish height... Maybe placing a Block, Huge on its side, and placing a block, large on top, making the bases an even [1 block and a half] height? Your help would be a ppreciated. Also, if you want to know a bit about the map, imagine Sandtrap, Valhalla, and Blood Gulch stuffed into a blender and dumped onto Sandbox.
Just try ghost merging a block to the desired height? Its hard to tell what you are getting at when there are no pictures, but if you need to cut the height down then just merge. If not, experiment with stacking like you are saying.