I normally keep five rods rigged on my deck. Two on either side and one in my hand. When not in use, I let the lure hang just outside the boat while the rod lays flat on the deck. This way, if I need to do a quick follow up cast with say a Fluke, I can drop the rod in my hand, grab that rod and make a cast without wasting time unhooking from a hook keeper or unwrapping the rod or lure.
I'll keep the rods on deck about six inches behind each other so the lines don't tangle, but when I'm moving from spot to spot with the big motor, I'll secure both the lures and rods before moving out. That's when the wraps, and or hook keepers come into play for me. If it's a short run, I don't bother with a rod or lure wrap, I just use the keeper. If it's a lengthy run, I'll either cut the lures off, or add a rod sock.
Don't be afraid to add some tension on the line when using hook keepers. Not so much that the rod bends excessively, but enough to keep tension on the keeper. The only way you damage a rod is by putting a bend in the rod, and then storing it that way.
One note on tackle organization. When I cut off a lure and replace it with a different color, style, or size, I don't return it to my tackle box. I'll hang it on the inside of my gunnel. At the end of the day, I have a better idea of how well I developed a plan for that day. If there's more than four different styles hanging there, I totaly missed the boat and re-examine what made me dicide to start with them. If there's a mirade of different colors or sizes, then I know my lure selection wasn't my downfall, it was not successfully locating fish.
Next time out, I'll have a different plan as to lure selection, and or possible fish locations.