Do NOT drill into the trunk. The harness should come with 2 little question mark shaped plastic pieces to hold down the harness coming from the side cover to the right speaker. Then it goes under the passenger backrest( 3 nuts to remove in the trunk) and into the left speaker housing to complete. 2 beer job at the most.

Yes, it can be done that way... much easier. The only problem I had was that the harness from Electrical Connection had a LIGHT GRAY covering on it instead of the black as shown on the picture on their website. If I would have mounted it external of the trunk it would have stuck out like a sore thumb.
I changed it into a 4 beer job (iced tea in my case) and drilled the bottom of the truck, the inner trunk liner (near the two tabs at the hinges), and the trunk lid (near the hinges) into the back of the speaker pods. Little more work, but very clean install in my opinion.