I'm not sure what you are trying to describe, but I doubt that the thermostat housing is in the heater hose line. Start by asking to see a diagram of the cooling system hoses. A parts store listing may not have that and if they cannot determine what you need from their catalogs, you may need to visit the dealer.
As far as how to protect the new hose, just do whatever is needed to keep it out of harms way. Sometimes you can cut a piece of the old hose and attachet it to the outside of the new hose with duct tape or silicon gasket sealer as a guard where the hose had been rubbing. Sometimes you can use tie straps (nylon wire ties) to hold the hose away from what it was rubbing on. Sometimes you can keep it out of harms way from simply properly orienting the hose and trimming it to the correct length.