You can buy or build a holder to put them in the vertical posistion...after having both...I LOVE the vertical position of the rods...they are much easier to deal with and get to. If you can put them width wise in the boat...and not front to back. I have done the front to back thing and the lines can still get tangled. Although its hard to find a good place to go widthwise and not be in the way. If i did it again I would place them across the back of the boat. There is a Triton on the boards I've seen done this way. Put some thought into it and add them. I wouldn't go into the floor though..just my .02 cents. I like leaving things intact...just me though. Post a pic so we can help you on your design.
"But if serving the Lord seems undesirable to you, then choose for yourselves this day whom you will serve, whether the gods your ancestors served beyond the Euphrates, or the gods of the Amorites, in whose land you are living. But as for me and my household, we will serve the Lord.” Joshua 25:15