You may write 'Original Submission' on the top of the letter and 'I-539 Submission' on the envelop. If you submit original I-94 (says in the i-539 instruction) you might want to make a copy for yourself. It is always a good practice to make a copy of all the paper work you send to USCIS. For your parents, you can just use one I-539 application (one as main applicant, the other as dependent applicant) and one application fee ($195 instead of $140 if you submit it after 4/30). If you send any copies of originals. You may want to include a statement saying that 'all material submitted are true copies of original. I understand I may need to sumbit originals if requested by officials'. By the way, I would use at least Priority Mail (with delivery confirmation) or Fedex to submit the application. Good luck,