rewiring question

OK, the bike is going back together s l o w l y , and I'm already thinking about the new wiring harness. So, I have a question for any of you who have wired a bike from scratch:
I'm looking at having the frame-mount fairing brackets easily removed, and having a quick-mount setup for a regular headlight/turn signals. So it's going to be darned inconvenient to have that rat's nest of wire connectors in the headlight bucket. I'm planning on building an underseat case to hold the new MegaSquirt unit and all attendent connectors, so I'm thinking of routing all the harness connectors there. Is this practical?

sure its possible,are you going to run seperate wiring harness for the lights that are mounted to your fairing so you dont have to undo the rest of your wiring harness to get at it?