I've had that clock for years. Except for mode 16 ("Up to 4 Time Controls with Bonus time per move, manual set with/without move counter", as described by the manual), there is no way to tie the move counter to the time controls; the way it works in other modes is that whenever a player reaches zero, the time for the next time control is added (to both players) and the flag falls. It is then up to the players to check whether the requisite number of moves took place, and decide whether to continue (the flag will disappear) or claim a win on time.
While it may seem like a missing feature, I would argue that the "letting the flag fall and have a human check the number of moves" approach fits better with the rules for tournament play, because the only authoritative source of move count is the scoresheets, or in some cases, a tournament director or their deputy witnessing the game (for an exception see footnote below). For example the USCF rules say "move counters, on clocks equipped with them, may not be used as the only evidence in claiming that the prescribed number of moves were not completed in the allotted time". A good rule in my opinion because players don't always use the clock reliably.
My advice: ignore the clock's move counter altogether.
Footnote: there is one situation in which the move counter is actually authoritative according to the USCF rules. When there are less than 5 minutes left, a player who is planning to claim a draw under the 50-move rule can ask the TD, who "may insert a clock with a move counter that shows the remaining time of both players, set the move counter to zero, and order play to resume. When the clock indicates that both sides have completed 50 further moves, either player may claim a draw. If this method is used, the director should inform the players that if a move is erroneously not counted or double counted, the players should stop the clock and notify the director."
