I made my reefing lines run a lot better by doing a Amsteel to XLS splice using these instructions:
Splicing Amsteel to Sta-Set
The portion running through the sail is 3/16" Amsteel. What runs back to the cockpit is 3/8" XLS. When the reef is in use the splice ends just at the clutch. This has made the single line reefing work well on my boat and it's nice not having a heavy line running up and down along the sail cloth. The Amsteel slips nicely through the reefing grommits on the sail. It also doesn't stretch.
I'd say keep it simple on what you run back. On my boat I have a dodger and the following run back: outhaul, reef, main halyard, vang, jib halyard, spinnaker halyard. This is how the boat came setup (except for the vang, which I added). The only control not run back is the topping lift, which is forward under the boom. Furling and spinnaker tack line both run back too, but along the stanchions.
I setup my previous boat and only ran the two halyards (jib was hank on) and reefing lines back to the cockpit. Topping lift and outhaul are on the boom. Spinnaker halyard is on the mast. Vang is at the base of the mast and is accessible from the companionway. It's less cluttered and still pretty easy to access everything if single handing with an autopilot. It's also easier for guest crew to figure out.