I would do it one peice horizontal. Make a template of the side of the boat before designing graphics, the graphics will migrate up, in the front, due to the shape of the hull.
Actually, the graphics only
appear to run up toward the front. There are some crazy compound curves at work there. If you were to flatten out the sides of a typical bay or bass boat, you would find that the graphics actually need to run
down toward the front in order to appear straight when applied to the boat.
You definitely need to make a paper template if you are doing anything other than a pattern... like camo or whatever. We use low tac transfer paper. Lay the paper on the side of the boat and trace out the edges of the surface to be wrapped. Be sure to mark any obstacles. If you have a basic design idea, you could even sketch it out on the transfer paper. If you have text or a logo that will be placed toward the front of the boat, it is crucial that you figure out where it needs to go on your paper template. When you're finished marking it up, pull the paper off carefully (this requires at least 2-3 people) and stick it flat onto a wall. Mark off a 12" reference measurement, stand back from the center and take a picture. Bring that pic into Photoshop and scale it up to full size. There's your template.
When it comes time to print and install, you definitely want to do it in one long horizontal panel. You also definitely want to use 3M 180cV3 as it is rated for marine use. If all else fails and you have to do it in vertical panels, make sure you start in the back and work your way to the front. This will ensure the seams aren't overly succeptable to the punishment they are going to get from the water at 40+ mph.
Good Luck!
Andrew