Use a rubber membrane in the valley under the shingles instead of metal flashing and then install the shingles to match the photo below. This creates even heating in colder climates with snow while the exposed metal keeps melting and causing ice buildup when the sun hits it.
The image to the left is an example of how a valley should be done. You continue one side of the valley shingles up a couple of feet past the other side of the valley and then bring the other side over and cut them off in a nice straight line. This creates a much better look as well as a leak-proof valley. With the rubber membrane under the shingles as added protection if any water did manage to get in there which is highly doubtful, it would just drain out into the eaves trough.