To me, the choice between Quantums or Photons comes down to this:
If you're going to use them every time they're off CD, whether shields are down or not, use Photons. If you're going to only use them when shields are down as burst hull damage, Quantums.
As for mixing beam types; don't mix beam types. Phaser Relay consoles have a higher bonus than Directed Energy Manifold consoles, and putting your points into one beam skill is more efficient than putting them into several. Phasers are the MOST efficient use of skill points, but there is something to be said in PvP for not outputting the same kind of damage everybody else is expecting.