Planning a story, eh? To me that's about 90% of the process, so I can't possibly go into all that I do here. But the headlines are:
There are four crucial tentpoles for your story - the inciting incident, the end of act 1, act 2 and the end point of your story. You need to get these in place very early on.
Once you have them, then give your hero, your villain and any other major characters their own column in a spreadsheet, and give your four tentpoles their own row, spaced out down the left hand side of the spreadsheet. You then have a software equivalent of a whiteboard that is incredibly easy to work with.
You should then just fill in your story between these tentpoles, one beat per cell. Don't be afraid to change the tentpoles if you have a better idea.
Once you have your grid filled out, you can build a single column list of the story beats, all in the right order, and that gives you the basis for your treatment.
Feel free to email me if you don't get what I mean and I'll explain in more detail.
Phil