In today's navy, Combat Information Center has a watchstander in verbal communications with another on the Bridge. The Helmsman or Lee Helmsman has headphones to talk to Engineering about speed. The Lookouts talk to CIC and the Bridge phonetalker. Aside from this, there's some bitchboxes for the OOD (Officer of the Deck), Conning Officer, and JOOD (if assigned) to talk to Damage Control Central, Main Control, Central Control Station (replacing DCC and Main Control on newer ships), Aft Steering, CIC, PriFly, and other locations. Then there's the 1MC, the all-ship announcement system.
In Trek, I assume that when the Science Officer or Comms Officer pinpoints someone for pickup, they either manually or automatically feed that data to the transporter room. If you have a communicator and call for transport, the computer feeds your location to the transporter room. If you call for multiple pickups with one communicator, then the Science Officer uses sensors to pinpoint the number requested. It is odd, though, when 5 people are standing there, and the guy with the communicator says "5 to beam up", one guys says "I'll stay behind", and the first guy says "Make that 4", and the transporter operator beams up the correct 4.
