Hotels, B&B´s and inns are usually set up as one property with a number of rooms. If you have several independent lodgings e.g. apartments or villas you can still set them up as rooms if it suits your marketing strategy. Each room (which can also be an apartment, house etc) can have its own pricing and booking rules.
Making different properties means each can have it's own property booking page (if required with individual design). You can also use an agency a multiple property booking page with advanced search functions (e.g. facilities, location) showing all properties.
If you're renting your property as a whole, you still need to define one "Room" which in your case represents your complete property.