Lately I do my rough planning on a whiteboard, then transfer it to notecards pinned to a physical corkboard to flesh it out, for example:
I've tried a lot of outlining software, but something about having a physical board is very motivating. It's also easy to rearrange plot points this way and put things in whatever location you want, see the whole thing at once, etc. Scrivener has a corkboard thing as well, but I haven't actually tried that one.
As far as story structure itself goes, I recommend reading Save the Cat by Blake Snyder.