I would not bother crossing lines. Standard cockpit drains are too small anyways for serious blue water work. If I had all my druthers I'd have an eight inch checked drain out the back. (look at one of the Coast guard RIB's) The ones with the 50 calibre mounted in front!
The reason for not using schedule 40 or 80 PVC pipe is that it is too rigid and you must allow for some flexing between the cockpit floor and the hull.
I have 1 1/2" re-enforced neoprene fuel hose with barbed and clamped bronze fittings and thru hull. There is one on each side of the companionway in the corners of the cockpit. one elbow (90 degree barbed) and one "T" leads to the single through hull which is just above the waterline. This was factory on my Seafarer 29.
Re crossed drains. The lower cockpit drain would not drain when heeled anyways. The outlet would be higher than the drain. The upper outlet won't have any water near it.
The hose is available from most autoparts stores (NAPA in my case). Use fully stainless hose clamps (hardware store NOT automotive) and double them up. After installation put a bit of silicone adhesive sealer on the screws so that they cannot work loose. You could also use reinforced auto radiator hose as that will safely last ten years or better out of the sun.
My Seafarer 22 has only one drain in the center of the cockpit that is lead straight down to a through hull in the centerline. Hose again between them.
Seafarer 29 KCB