Rule #2: If it’s a mess now, it will be a mess later. (So fix it!)
This rule exists to save time, even though a superficial examination may initially seem to indicate otherwise. At some point, the nice stack of rope that you’ve been working with or the well-organized anchor you’ve constructed will become a mess. While it may seem faster to just try to muddle through, the best option is to stop action, re-flake the rope, and re-organize. All it takes is one experience hanging out at a terrible stance fighting the pump on the lead as your belay attempts to disentangle the Christmas lights-style knotted pile of rope to become a believer in this rule. So, if the stack is untidy or the ropes are twisted, fix them first, then climb on.
The corollary to this rule is about preventing messes in the first place: order your anchor like the world that’s tied to it. If you wish to keep your ropes running free and clear, avoiding twists and tangles at the anchor, the best advice is simply to keep everything clipped to your anchor in the same order (left-to-right or top-to-bottom) as the things (usually people) that are clipped to it.
For example, suppose Tom, Dick, and Harry are multipitch climbing together on two ropes. Tom is leading with both ropes, Dick is tied to one rope and climbs first, and Harry is tied to the other rope and climbs second (1). Starting with the first pitch, if Dick is standing on the ground to the left of Harry, then Dick’s rope should be tied in to the left of Tom’s belay loop. Similarly, Harry’s rope would be tied in on the right side of Tom’s belay loop.