N.Y. Comp. Codes R. & Regs. tit. 9, § 6210.9 – Vote tabulation.

(1) Ballots shall be reviewed pursuant to the provisions of section 6210.13 of this Part, to determine if the ballot is machine-readable or if the ballot requires that it be manually counted, then recorded in the official canvass of the votes for the election.
(2) Ballots shall be assembled in separate batches by election district unless otherwise directed by the county board to preserve the secrecy of the ballot.
1. (i) Each batch shall be identified by a header card and at the end of all batches there shall be an end- or trailer- card, if required by the software. Header and trailer cards shall be visually distinct from ballots. Such distinction may be made, for example, by using a different color card stock, or different edge marking, or by other appropriate means.
2. (ii) The bi-partisan team of county board personnel shall place header cards, in order that the votes recorded on each ballot shall be attributed to the correct election district. When placing header cards, as each is placed by one person, the other person shall verify that the header card is the correct one for the batch of ballots which follows it and that it is correctly oriented in the batch.
(3) Ballots shall then be fed into the central count paper-based voting system. Following the counting of all ballots, a tabulation report shall be printed. Two back-up copies of the tabulation report shall be locked in secure storage.
(4) Where the number of ballots to be canvassed is small, the county board may provide for canvassing of the ballots by larger units of representation.
(b) Testing during ballot tabulation by central count paper-based systems.
The system shall be so designed and constructed that, at the discretion of the county board, it shall be possible to halt the ballot tabulation at a point when a portion of the election districts have been counted, and run the test deck to demonstrate, as in the tests listed in section 6210.2 of this Part, the accuracy and dependability of the count without interrupting or affecting any official tabulation of results that may be on the equipment at that time.

(a) Preparation of ballots for tabulation by central count paper-based systems.