What are the best ways to stay organized during the application process?
1. Narrow Your List
In the fall of your senior year, you should create a narrowed list of schools to which you will apply. Keep the final list small (6-10) and balanced (equal number of likely, 50/50, and reach schools) for your sanity (and the sanity of those around you).
2. Make a Chart
When this list is finalized, make a chart to keep track of supplements, deadline type and date, sending standardized test scores, working with your school counselor to send letters of recommendation and transcript, scheduling and completing an interview, etc. No need to reinvent the wheel, check out this great sample from College Board: http://www.collegeboard.com/student/apply/the-application/8435.html
3. Check it Twice
Put the final chart on the fridge (or some other central, regularly viewed location). Check tasks off as you complete them. Create a once-per-day, very short "check in" routine (before bed, when you get breakfast, after dinner) to review your deadlines.
4. Take Help Graciously
With your chart prominently posted, others (parents) will likely create a routine of checking-in (probably more than once a day). Take the reminders graciously (yes, let them nag).