I used regular first class USPS for secondaries. (although I used a catalog envelope, so I needed two or three stamps.) Then I just called each office to see if they had received it. I sent over 30 packets.
Each packet had a bar-coded ZIP+4 mailing label courtesy of a labelmaker I had at my office. I don't know for certain if this helped the envelope get through, but it looked nice.
I used a spreadsheet to track the latest update I got from each school as the process moved along, and a windows addressbook to record phone #'s, addresses, URLs, and username/passwords.
In most cases the only material I sent was photo/resume/signature/check, because the secondary content was sent over the web. About a quarter of all schools took payment via credit card, so I didn't need to send a check.
All the offices received my USPS mailed stuff without a problem. The only delay came from the LORs, which were sent via email by my premed office (PDF file.) A few schools lost the email and needed it resent.