The first thing I would suggest would be putting some 1 & 1/2" extruded styrofoam board under the deck, for added rigidity, noise/vibration dampening, and flotation in the event of being swamped.
Then, I'd run the wire harness through some 1/2" flex conduit, or gray PVC conduit (use gray, not white, gray is rated for UV exposure and is more durable) Not sure how many wires you have, or what AWG you're using, but a 1/2" conduit will hold at least 6-8 AWG 16 wires, because it will hold 3 AWG 10 wires (there's a chart somewhere that will tell you this info) If you've got a lot of wires, you may need to use 3/4" conduit, or an extra run of the 1/2"
I know you said you want to go cheap, but when you start doing your wiring, buy quality and only cry once. Make sure to use marine grade wire, and anywhere you make a splice, you need to use adhesive-lined heat shrink terminals. They're about a dollar a pice at a marine supply store, and a helluva lot cheaper at an auto parts store for basically the same thing. Also a good idea to wrap each connection with some 3M splicing tape.
Wherever the wires are not in conduit, it's a good idea to use some split loom, and a wrap of friction tape every few feet along the loom to keep it bundled together.
Regular electrical tape has NO place on boat wiring, it's as useless as a set of double D breast implants on a boar hog. Soon as it gets warm, or wet, it gets gooey, and begins to unravel. Save this type of tape for home wiring, and only use splice tape, friction tape, or heat shrink tubing on boat wiring.
And if you REALLY want the wire harness to look and function like a factory harness, buy some delphi multi-pin connector plugs (they sell kits) and use these.
If you do all of this, you will have a wire harness that will last many years, and will meet ABYC standards, which is important if you have to insure the boat, as underwriters will not touch anything that doesn't meet industry standards.
