Banks haven't issued negotiable certificates for years. They issue receipts for a deposit into the account. I'll bet your "certificates" say "non-negotiable" somewhere on them. Consequently, we can redeem the funds in the account without having the piece of paper or completing a lost certificate affidavit.
The BSA defines negotiable instruments to be "Personal checks, business checks, official bank checks, cashier’s checks, third-party checks, promissory notes (as that term is defined in the Uniform Commercial Code), and money orders that are either in bearer form, endorsed without restriction, made out to a fictitious payee (for the purposes of Sec. 1010.340), or otherwise in such form that title thereto passes upon delivery. Chapter X 1010.100(dd)(1)(iii)
The $15,000 in cash for a certificate of deposit would be reported as a "deposit" on the CTR.
"Payments" are generally used for loan payments, safe deposit rental payments, etc. I would personally list the $2.00 using "Other" and specifying "Service Fee."