Like many others, I just roll up the lines with the tarp and pull the snake skin over the whole shebang. My stakes go in a separate pouch.

What's made life easier for me is multi-colored guy lines - either two colors (one side or one end is distinct from the other), or a freakin' rainbow. If they get tangled, it's much easier to see and separate, and since you can see, they're less likely to get tangled in the first place.