We have a Valor so it has the Flair-it manifold system instead of a nautilus but I just have brass 90's with quick connects on them for the inlet and flush ports. Only threading on is at the water source for the splitter/regulator setup.
Short 4' length of hose connects inlet to softener that is placed under unit. Our clearsource filters are hard plumbed in and fed from the water inlet so any water coming in, either straight to fixtures or filling the fresh tank, passes through the filters. I don't love this as the water sitting in the tank is not re-filtered before fixtures but it hasn't given us any issues and we were more often on city water when I installed it.