They are intended to run down to the turning blocks and into the cockpit.
You should have one/ two rope clutches for easy reefing.
I will try and explain. Lines are led from the luff grommets which become the foot clew at each reef point through the end of the boom to the mast end of the boom to the turning blocks back into the cockpit through the clutches.
You should have a dedicated winch ( or sometimes the main sheet winch) on the port side which pulls in the reef line.
Its as simple as dropping the main halyard to the sail tack point, attaching the reef tack ring to the reef horn at the mast, tensioning the halyard , pulling in the reefing line attached to the reef clue on the luff. Make sure you do it in the proper order or you could rip the sail.
Practice this at the dock in calm winds.