heavy weapons in phaser hp will work normaly.phasers in heavy hps wont be charged normaly. they are not attached to the phaser capacitor. lets say u have 2 phasers in phaser hps and 2 phasers in a heavy hp: your phaser capacitor will only charge enough energy to fire 2 phasers. u can fire whatever phaser is pointing at the target but after 2 shots u will have to recharge. so basicly a phaser in a heavy hardpoint is an emiter your "real" phasers can choose to be fired from.at least thats the way it works in sfc2 op.
with some carfull moding of firing arcs u can built a ship with lots of emiters covering all arcs but with only a handfull phaser weapons.can help balancing the shiplist. i think thats the way they should work in trek anyway. the tmp enterprise has 18 phaser balls but it never fired more than two at a time although other emiters should have been in perfect firing position as well (the mutara battle in twok)
maybe the enterprise only has 6 or 8 phasers wich can be fired from whatever emitter is in perfect position.
hope that helps
ed