York, Generally the floor joists are morticed in to the Tie beams or girts so that the tops of the joist and beam are flush to receive your T&G flooring. If you are using the room above for storage or a spare room, place the joists on top of the beams raising the floor the thickness of floor joists. This will allow you to place recessed lighting between the floor joists and you can sheet rock or T&G the bottom of your floor joists, leaving you fully exposed beams. Most new recessed lighting have cans that are 4",5",or6" deep that will work in your application.
Good Luck, John