I leave one clip on the plane and both clips on the handle. No color code BS. Three of the clips are standard Sullivan (or Brodak or whatever, all identical). One clip is a homemade item made on the Derek Moran/Jim Lee clip bending jig. I typically have my dedicated handle and primary set of lines in a 1 gallon ziplock freezer bag. In a small plastic bag is another set of lines, also in the gallon bag. If I was real serious, I'd have the clips sorted out for those, but I haven't yet. Someday, maybe.
My theory is that if you rely on color codes, you'll eventually grab the wrong set of lines and you've set yourself up to lose (not loose) a plane. I also see no sense in dragging your uber light CF/balsa handle across the asphalt when there is a nice heavy stunter sitting there with two sturdy leadouts to act as an anchor. Hook the lines up, roll them out, hook on the handle. I pull on the lines and seek the 'up' line and hook on the 'up' clip that's already on the handle. Then, the bottom clip. DO NOT look at the flaps, only the elevators. I hold 'up' and look at the handle, then look at the elevator, then the handle, then the elevator! Well, early AM, anyway. As an added bonus, at a contest, I can remove my handle, roll the lines up to the leadouts, and leave them attached to the plane between rounds, likely saving them from damage in the pits. When you're done, remove the handle, leaving the clips on it, wind up the lines and remove them from the plane, leaving one clip on the plane. Put lines and handle in gallon ziplock bag, and put it into the tool kit. Done deal.
Paul has one of his lines (and one of his leadouts) about 5" longer than the other. This ensures that the clips won't snag together and also is a dead giveaway that you've obviously hooked the lines up wrong. He leaves the handle attached to the lines. That's the only part of the system I don't agree with. I think it's too bulky to pack and also harder on the lines, but otherwise, I think it's a great plot. There's really no reason to have a problem with this.

Steve