As a second time applicant, I have learned the right and the wrong way to apply. First off, start working on your personal statement around february or march. Finish it a LONG time before you need to turn in the app. Secondly, start working on the online app the second the online application is active. At least put in all of your classes and activities. At this time, not many applicants have started entering the data, so the app shouldn't be slow. Also mail off your transcripts to AMCAS in early may and call to be sure that they have them. Preferably, call before the online app is able to be turned in so you won't be on hold for an hour.
I definatly would turn in the app on June 1st. It should be done about a week before that. If you procrastinate a long time, you could be SOL because everybody will be online at that time. Your goal is to only have one thing to do on June 1st. Maybe cut and Paste in your essays. BUT DON"T LEAVE THE THINGS THAT TAKE MANY BUTTON CLICKS UNTIL THE END!!!!! Also, if you are invovled in many activities, be sure to be very descriptive in the place provided. For example, your research. This is the only place that some schools could get an idea about your research before they ask you for an interview.
I turned in my letters of rec to all the schools a week after I turned in my primary application. I thaught it would take our Pre-professional office three weeks to mail them, it took 2 days. Not a single school threw away the letters of rec. I didn't send the letters to the UC's or university of Mich, because I knew that they ask for them later.
I then found a friend who applied the year before. I took all of the secondaries that he had on him from last year from schools I was applying to and started working on all of the questions. I finished about 80% of the questions when I started getting secondaries. I was able to have the questions read by someone else and send out the secondaries within a day. Then I called the schools a month later if I recieved no indication my apps were complete. Use Excel to keep track of everything. I think that's everything. Hope this helps.