How to flash a roof valley on parallel roofs
Since you are redoing the roof deck, you are at an ideal time to fix this right, or as right as you can without redoing the major framing.

Depending whether you want the water to all go one direction, or go two ways, you build a flat (but sloping) triangular roof in the valley - either raised at least one foot and sloping all the way to one end, or raised at least 6" in the middle and sloping both ways.Cover with ice and water shield (first) and metal flashing in a wide continuous sheet running up both roof slopes. Essentially, you are giving this valley floor some slope - to do so you have to give it some width as it rises from where it is now.