I just finished reading GTD and don't understand the mechanics of how you relate the NA lists to the original projects lists generated by the in- basket filling and "triggering" ideas listing. Once you have your projects, figured out 2 or 3 next actions for a project, placed one on the appropriate NA list, and completed it, do you cross it off the NA list and immediately return to the projects list for the NA for that specific project? Where do you keep the other 1 or 2 NAs that you have figured out but haven't written on an NA list?
Also, where exactly do you keep the project source material- in a separate filing system from the alpha one?
Finally, are random notes about agendas and other writings kept in the reference system or with the project resources and do you integrate the project files in with the alpha filing system or keep them separate as well?