What I started doing a long time ago is building a room based on need. I take some dirt and consider those my machines, then make walls and floors with cobble. So, bottom floor, is Thaumcraft, two small storage rooms, factorization, nether portal, mining shaft down, and finally a bedroom. After laying it out, build up 3, and roof it. Now, you 'can' end up with a square house, but you don't have to. Add in things like bay windows, lofts, attics, pitched roofs, etc. That said, here is where I really, really wished the builder actually worked.