There's my rig. It has 5050 LED's on the inside and outside. I drilled holes in the hull at the front to pass the wires through. Drilling a hole in the hull of my less than 1yr old boat was one of the toughest decisions I've ever made. I went thru closer to the bow because that is the driest area of my hull, and I didn't want wiring running around the stern and over the transom, I could just see that getting torn up somehow.
I used 3M black weatherstrip adhesive to stick mine to the underside of the gunnel extrusion, and a little over 2yrs later they are still holding fine.
My suggestion is, and most people have them mounted this way, to put them on the under side of the gunnel pointed downward, not on the side of the boat pointing outward. You'll get better light penetration into the water, and the lights will be less offensive to other boaters.
On the GW stopping you while running them at night, my experience was different. I got checked at Tawakoni just the week before last at about 10pm. A buddy and I had just left the fishin hole headed back to the ramp when the GW lit us up. Yeah, they were being sneaky and crept up on us in the dark. I had just gotten on plane when he lit my buddy up (who was behind me), so i just stopped and waited my turn. After they checked all the safety gear, licenses, and fish, I asked them about me running my LED's while underway. Their opinion, and they did say that every warden might have a different opinion on the matter, was that since mine were mounted in such a way that they could still see my navigation lights, they didn't see how mine were an issue. If they were mounted in such a way that they over-powered the nav lights, he said I would have gotten cited for them. Made perfect sense to me.