The two roofs are connected by siamese tubes and drain out behind the front and rear wheels just like any other typical Nissan. When the drain rails overflow on a Quest, the water usually heads down the headliner to either the A or D pillars, depending on the incline of the vehicle. When it comes down the D pillars it ends up in the rear well. Nissan's documentation for drains is deplorable in general, but you can get some idea of how they run from the diagrams here on pages RF-43 and RF-45...
https://www.nicoclub.com/service-manual ... 2%2FRF.pdf
...and the rear roof parts drawing here:
https://www.nissanpartsdeal.com/parts-l ... m=736_A002
Rear drains are almost always best cleared from the bottom up, because clogs almost always happen at the bottom, plus the top holes are always inaccessible under the roof pane when the roof is open. That means taking the cargo room side panels loose on both sides, blowing or snaking out the tubes from the bottom, and poking a screwdriver through the bulkhead fitting from inside to dislodge any gunk and break off any "splash nubs" that may be molded into the fitting.