You might try looking into something like the Freytag analysis: [link] It wasn't really built for novels or short stories specifically, but it can be a helpful way of organizing a plot or simply thinking about how the plot functions.
If you're getting caught up in the detail and the story is getting messy, my suggestion would be to step back and try to break the story down into simpler pieces. What is the central conflict? What complicates or impedes resolution of the conflict? How does the protagonist resolve it? Getting this kind of focus will help you figure out what details aren't important and what will need to be cut or added in revisions.
Plan before you write. It will help you keep track of all plot threads, keep the pace good, and know where you want to end so that you can build up to that end in a well organized manner that doesn't feel rushed.
Try organizing the story before you start so you know where you want to go and where you want to end. My stories got a little more streamlined when I stopped on going into far out unnecessary detail and started thinking about what was relevant to the plot and what was necessary for me to go into and planned just a little bit more.
It also took me writing six novel sized stories to realize it and another three for me to get what I wanted. It's something that takes practice and you identifying what needs to be there and what doesn't. There is also revision. That clears up a good bit as well.
Revise, revise, revise. Then, revise again. Each time you go through the manuscript, you'll find ways to strengthen it - words that can be cut, scenes that need to be reorganized, holes that need to be filled in. Sometimes it just takes a few rounds to get a good handle on the plot and its delivery.