my roofing contractor did this. where the 2 pieces come together he made a long piece of flashing, put it under the main roof, and on top of the patio roof, the water slopes off pretty well, even in torrential rain storms that west texas is known for in the spring, but i had him fill the holes up in the roof panel on the patio roof side with roofing sealant just in case we get snow fall, because the water will want to back up.
i havent had any leaks so far and its been 2 years since i had roof installed.