I would like to know how I can enclose 1/2 of my garage so we can heat the side with the vehicles in it? I know to insulate/vapor barrier walls and ceiling but I am wondering if I need to close off the rafter that my new wall will be underneath?
There is no need to close off one section of the new attic space from the rest of the open space on the un-insulated side of the garage.
The whole area above can be left open.
Just be sure to put the proper R-factor of insulation in the ceiling and walls not siding on the heated portion of the house.
So long as your garage is finished already as James points out (ceiling already drywalled) then no. If it's not, then yes you will need to drywall the ceiling as well and ensure proper R-factor insulation is used.
A word of caution though. Garages are unheated and cut off from the living space for a reason. You cannot have exhaust gasses exposed to the interior of the home. Which means you cannot carry your HVAC into the garage to heat it where the cars will be parked, this is very much against Building Code and a very serious health hazard. You risk carbon monoxide exposure as a result. You will need to use some sort of electrical heating source for this portion of the garage to heat it to ensure it remains sealed off from the living space.
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