If you don't do it at the teller line, that means you are not delivering the notice at the time of deposit. Be prepared to refund those overdraft fees when 99% of the checks that you place holds on are actually paid.
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I am assuming you are only referring to the Reasonable Cause Hold Notices or an Exception Hold where you doubt the collectability of the check? My understanding is that the other Exception Holds (ex. large deposit) is not applicable to this footnote found in the Appendix C.
We do both as well. We are about 500m. Most of the decisions to place exception holds comes from our Ops and they review all of the holds that go on. We flag the account so that the tellers know when they should place holds on items.