Start small, build it up from there.

[He's eavesdropped on the starts of other conversations here and the logistical problems have occurred to him, too.]

If the system can be tricked into accepting a structure as a shelter, there's some threshold at which it's considered a building. Could be all you need is an enclosed space with a door -- build that and expand it when you can get more materials to it.

But the spiders service the buildings through the vents. It'd need to be positioned somewhere they have access.