It's a mix of things ...

lines and pairings are usually set before game/period and the coach calls them out/taps. (UNH's former coach Dick Umile used to whistle - annoying). Often one AC handles the F and one the D. If adjustments are made, that generally gets communicated by the coach. And then there are partials - where a change is called for and the guys on the bench know who (by position) they switch for, even if one or more can't get off the ice because of where the puck is (usually guys on the ice know to signal they're coming off).