Should I recharge entire portals or individual resonators?

Solution 1:

There is a current bug that makes you lose XM if you recharge all resonators while not all of them need XM.

Besides, when selecting a specific resonator you can recharge the important ones while you allow low level resonators to fail to allow for a new, filled up resonator to be deployed, if there is somebody at the portal site defending it (may be yourself). You waste less XM by placing resonators than by recharging them.

About AP, it is the same (bugs apart), since you may need (say) 5 recharges to each resonator (40 recharges) or 40 recharges to all resonators at once in order to fill them up. Both methods grant the same amount of AP.

Solution 2:

Yes, you can do that.

The best way is to recharge the whole portal until one resonator is almost full, then charge that resonator once (which should take up hardly any XM), repeat until done.

Of course, the value of "almost" changes with the number of resonators still to be charged, and with their level. Experiment.

Ideally, you can get another 70 AP with this method, though 40 are more likely.