You'll get a feel for it.
While the Priwen Burst is charging, you are invulnerable. This means you can use it as a split-second phase cloak at low flux, and also "pump up" your flux level on demand. The chargeup time and blast strength both depend on your flux level upon using the system. The system also builds flux when you use it, meaning you will indeed overload if you use it at very high flux.
The blast gets stronger in every way (area of effect, damage, knockback) the more flux you have when you cast it. The idea at high flux is to use it at near-max flux, so you get max power and get to vent or retreat after everyone gets crippled by the massive EMP, knockback and damage.
Generally you'll be safe if you don't use Priwen over 80% flux, but the "sweetspot" right before you overload is very rewarding...
Importantly, your Lattice Shield is disabled for a while after using Priwen Burst, depending on how strong the blast was. This makes it important to disable as many enemies as possible. Of course, if you're already at super high flux, your shields won't be online anyway, so you might as well just gun for it.
Managing Priwen usage is much the same as managing your shield on a standard ship, but it's a lot more aggressive in nature. When flying a Templar ship, your overwhelming power is the best defense.