When you first open the secondary application, the directions (from what I recall, at least) tell you to copy and paste from Notepad. I do not recall it saying to type it directly in notepad. Once I saved some personal/demographic information on to the secondary, that warning page disappears and does not come back. I originally typed my essays in Word, pasted them onto Notepad and saved the documents as notepad files. I then copied and pasted from Notepad onto the secondary. As I was about to submit the secondary, I noticed some formatting errors in "print preview" even after I copied from Notepad. Apostrophes, semi-colons and quotation marks all turned into question marks.
Upon seeing the errors, I had to re-read all three essays and manually fix the out of place "?"s with the proper symbols, which was the only way (for me) to fix the errors despite following the original directions and advice given here on SDN. That seemed to fix the issues, however, my paragraph indents were sometimes lost, but I figured that with all these formatting issues this application is causing, the random loss of indentation isn't a big deal.
Sadly, they won't fix or let you fix any of your secondary if you have submitted and paid for it. Hopefully you didn't use a lot of quotes, semi-colons or apostrophes, otherwise I think the essay readers will just look past the few errors.