Applying to graduate school takes a slightly insane level of organization. Luckily, since you've made it this far, you're already tremendously organized and you don't need any tips from me. (I hate it when people try to tell me how to organize my things.) However, just in case you're interested in what folders you might want to create, here's an example of how I organized everything. Take it or leave it!
My highest-level folder structure is as follows. Anything that doesn't have a .doc / .xls ending is a folder.
0_GRAD_SCHOOL_MASTER_SHEET.xls: This excel sheet was my most important document. I had schools in each row (and the NSF scholarship / Gates Scholarship apps), and a bunch of column labels. The column labels were as follows.
0_Professor Letters.doc: Next I had my "Professor Letters" word doc, in which I drafted the emails I sent to every professor. I recycled a lot of material, but I needed to insert / delete sentences or paragraphs specific to each professor's research.
1_Prep by School: Then the "Prep by School" folder, which had a separate folder for each school. Within each school folder, I had:
2_Final Essays: The "Final Essays" folder just had the essays for each school, as well as my diversity statements, writing sample, and final CV.
3_Interviews: The "Interviews" folder had all of the technical information about transport, downloaded pdfs to read on the plane, and my schedule.
4_Acceptances / 4_Other Decisions: And the "Acceptances" and "Other Decisions" (ha) folders are self-explanatory.
Hope this is helpful!