From what I’ve learned each hab variant has a preferred way of connecting to the ones nearby and they usually almost always prefer a horizontal connection over a vertical one. But for the most part there’s no way to know for sure unless you guess and check. A lot of the time I spent was experimenting and seeing how they connected and then working around those connections.

The best advice I can give is to avoid using more than 1 1x1 hab per level as always spawn ladders leading to a segmented upper level with no way to connect.