I don't think there's any protocol. Just make sure you have some contract with them. It could be a paper you type up on Microsoft Word which you both sign. I think this is a good idea, in case they end up stiffing you and you need to go to court or something, but let's hope not. The big Hollywood places do contracts with locations for the same reason. The contract should mention that the deal is between your production company and them, and what you intend to use the space for and how much you'll pay and everything, so it's all set out before you do any shooting. Than you both sign it.
Other than that, I don't know any difference than just renting some space.