I know it's a little after the fact, but I thought I'd chime in with some suggestions (and echo some others).
I used to use dots in my book, but my current SM professor loathes them with every fiber of his being. Now we're required to use the pencil/ruler method and just go with it. I like it SO MUCH MORE. I'm very big on organizing my books and having things look nice (to the point to where I redo things later, which I need to stop doing b/c it takes too much damn time) and it just reduces the clutter 10 fold, and plus...dots fall off. I was calling a show and had three cues missed b/c my dots disappeared.
One thing that I'm very greatful the school I'm at is willing to do is that during tech, more specifically wet tech, nothing moves unless I say so. I know some places are hellbent on getting out of there fast, but I've managed to get the directors to see that sometimes you need time to work a difficult sequence and they understand, and we're still out of tech by 9:30-10pm most times.
Also, and again it helps b/c I'm in educational theatre right now, I tend to know the designers fairly well. On both shows I had this past year I knew the lighting designers very well (both undergrads) and there were two impossibly hard cue sequences in both shows (Mass Battle and MacDuff/MacB fight scenes in MacB and the blinding scene in Equus) so we set some time aside before tech or before the opening night show to run the sequence with each other so we could see how things needed to be timed. It really helped.
A thorough paper tech is nice too, but sometimes it's just not possible. Equus was a rushed paper tech b/c the director was an idiot and just "didn't get the point of doing it".
Anyway, hope some of that helps....but above all..SCREW THE DOTS!