I did it through an excel sheet. I made a list of all school choices, average GPA, average MCAT, secondary deadline dates, secondary costs, a next up box, and a status. In the status box I colored the box in with Green (accepted), Yellow (Interview), Red (rejected). The next up box was where I would put what I need to do next.
On a word sheet, I listed all the schools and bullet pointed how the process went. So most of it was "AACOMAS Application, Secondary, Interview, Decision". For this one I printed it out, placed it above my desk and I would cross stuff out when I was done. I correlated this with my excel sheet.
Advice: use interfolio. Have your LORs go to their so your professor/doctor only has to write it once. Once they submit it, you can just click off which schools you want it sent to and they keep backups. I would NEVER go through the Health Professions Office because I remember them loosing a lot of my letters. They also didn't like me too much because I wasn't a "top candidate". Also, keep a copy and print out all receipts for applications. Throw them in a folder just in case. I'm pretty cautious by nature. Lastly, if you don't hear a confirmation from the school that they got your application or secondary, call them up. Don't sit there thinking they got it. I have heard many stories of Admissions not getting something but the applicant thought it was fine.
Good luck and apply early.