It really was not clear to me either. I only found out about this requirement two weeks after submitting my application causing me to panic.
From their website:
"
Whenever possible, you must upload scanned copies of official transcripts to the online application. Please note that these must be official transcripts printed on university letterhead. Print-outs from online student portals are not acceptable.
After you submit your application and received your 10 digit USC ID number, you must also mail in official transcripts from all colleges, universities, and other post-secondary institutions you have previously attended. NOTE: If you are an applicant to a Viterbi School of Engineering program, please click here for specific transcript guidelines.
Cover sheet: We recommend that you fill out the “College/University Transcript Cover Page” and send it to the registrar’s office of each post-secondary institution you have attended. Although it is not mandatory, including it along with your USC ID number will help us match your transcripts to your file as quickly as possible."