the conduit capactities are how much energy can be sent to or drawn from the two batteries (main power and reserves), the limits are how much energy they hold (in %). weapons and sheilds draw from main power, several other things draw from the reserves, including the thirsty cloaking devices.
the idea behind designing this was resource management. you must balance the core power and how much the weapons, shields, sensors, and impulse engines draw (along with the draw from the cloaks) so that the ship doesn't immediately suck the batteries dry, leaving you with your pants down (shields collapsed) and quantums coming your way.
a general sample is that TOS ships generally need a core output of 800 (type one phasers being a rather light draw, apparently). take samples from the hardpoints of existing, working ships to look at and get a better idea.