Keep writing whatever comes to mind at the moment. I've never really thought about it before, but one thing you could do to stay organized would be to number the different 'parts' of your story in a word doc, then write down in a notebook where all the numbers are.
For example:
1.
[Scene where Terry and Jim go to taco bell]
2.
[Scene with Terry and Jim vs dinosaurs.]
Obviously those would be real scenes, or paragraphs, or however long.
And then in your notebook or whatever write the number and then a summary of whatever it is you typed there. That way you can look back over your notebook later and figure out how to organize your information.
... Actually, I might do this for my novel. My main character likes to jump around A LOT.
Anyway, good luck to you!