I know many people frown on using anything that isn't grey matter, but I found Storylines software quite useful on my last wip. It's basically index card software, but easy to shuffle and you can set up multiple 'lines' (that you can drag cards along) for each story - I used it for a visual way to track character pov (as you can see all the lines at once - sorry, it's hard to explain), but you could use it for subplots or perhaps structure as well.

I wouldn't use it for every book, but I was glad I had it to hand for the last one.