There really is no "standard" way to run the halyards. Beneteau typically runs the main and jib halyards to the port side of the boat if they are only installing deck organizers on that side. The jib would ordinarily exit higher on the mast to facilitate "jumping" it. Once out of the mast, run them through the turning blocks, deck organizer and then clutches in the manner that provides the freest run, preferably without any crossing.
If you are going to race or just want to set up like the race boats, then the jib and spinnaker halyards generally exit the mast to starboard. This is generally done to facilitate hoisting frequently changed sails from the high side of the boat while rounding marks. The main can go to either side since it is not changed during a race. Other control lines can be led in the most efficient manner for your boat and crew. Again, once they exit the mast and get to the turning blocks, the most free run possible is best.
On my boat, if you are interested, I have the lines run as follows:
Port side (from left to right) - jib hal, spin tack, main reef, main hal, vang
Starboard side (from left to right) - mainsheet, cunningham, outhaul, spin hal
I don't race, but typically launch the spin to port, hence the halyard on starboard.