I thought a desert temple might make a good base, so I started messing around with ideas in creative. http://imgur.com/a/2K5WO#0 The arcane stone next to the research table is intended to be an arcane infuser but with the first two blocks hidden in the wall for symmetry. I cleared out the two stairwells which I don't show, they could be used for other devices or to grow stuff. I put some storage in the level up above. As for personal space such as a bedroom, you could expand out the hidden chest area. Just remember to remove the tnt first. It took me a while to try to set it up. It's not perfect, I actually haven't played Thaumcraft 3 that much so it may not be fully ideal for it. Still, I think it looks cool and I really hope you like it.