Not sure I understand the problem either, but if I do...
Use a "drop down" hitch extension (made for tall trucks), but invert it, putting the ball on top of the extension. This will put the trailer hitch high and the tail lower, hopefully enough to get the back end under the garage door top. Of course you can't go high enough to allow the rear end of the trailer to drag. If this will work, you'll probably want to get a front receiver hitch installed on the truck to make visualization and maneuvering easier. You would only want to use this special extension for putting the trailer in the garage, not for towing.
If yours is a small trailer or a pop-up this may work. If it's a larger trailer it would probably be too hard and heavy to hook up and not safe to drive in. You'll just have to figure out the heights to determine the feasibility of this scheme.
