With my current project, I wound up in a position similar to what's described in the OP (I am impressively disorganized at times and I can never figure out how to outline), and I did some pretty weird things to combat it.
I didn't actually start a second draft before I'd finished the first, but I started writing lists and alternate scenes and short synopses of the altered plotlines. Basically, anything that seemed like it would help me organize the new ideas that were coming up, and help me figure out what was actually still going to be appropriate to the plot as it evolved.
My suggestion would be, if you're using a word processing program, make yourself a folder where you can stockpile your ideas as short, focused documents--don't get carried away, but this may help the confusion if you can give yourself a place to work things out and be ridiculous and write down your own thought process. (Of course, I also conduct interviews with my characters, prying into their personal lives and demanding that they explain themselves.)
As regards the actual WIP, what I did was, I wrote forward with the draft as though my new ideas had been there all the time, but I didn't actually go back to the beginning and add them in--that's what all the lists and alternate scenes were for. On the second draft, is where I started adding the new stuff right at the start.
This is obviously just my personal experience, and I would certainly not endorse it for anyone who has already figured out how to write a novel from beginning to end and have the whole thing behave itself
