Officer of the Day (OOD) and Quartermaster (QM) will pipe the side. QM will fall in aft side of brow facing forward while OOD will fall in forward side of brow facing aft.
They will come to attention, OOD will give the word of command, QM, PIPE THE SIDE! They should wait to the final moment before issuing the order as sometime the CO will wave off the pipe and indicate he does not want it piped.
QM will pipe the side while the OOD Salutes and the Commanding Officer (CO) will receive the side by briefly halting at the brow, returning the OOD's salute and then the CO will be escorted by the OOD to their cabin and receive a brief on the day's activities while enroute.
The other thing that happens is the 3rd Sub Pennant will be hauled down as soon as the CO embarks the Ship. The 3rd Sub is flown from the hours of sunrise to sunset to indicate when the CO is absent from the Ship.
Piping the Side is a funny thing, COs will generally tell the OOD when they plan on embarking but they will sometimes show up unexpectedly. The QM needs to always be maintaining a vigilant lookout for the Captain so as to alert the OOD if they show up unexpectedly. This is so the OOD knows to come to the Brow and pipe the side, or at the very minimum, greet the CO and brief them on what's happening onboard the Ship.
If the OOD is not at the Brow and the QM notes the CO approaching. They will give two short pipes in quick succession over the Ship's intercom to alert the OOD to come to the brow.