As far as running the jacklines up the side deck versus up the middle, I would argue that I want to
rig things in such a way as to minimize as much as possible the number of times I need to unclip and reclip in order to move about the boat. A double tether is good in that you can clip the second tether before unclipping the first, but the more you're messing around with your clips, the less you are concentrating on holding on and attending to the task that needed attending to.
Really, I would give a higher priority to making sure you have excellent hand-holds, great non-skid, and good toe-holds, and to developing your own agility and "technique" for moving about in a seaway.