I assume you are talking about the elemental percentage, correct (since Photon Arts are your special attacks)? Elemental percentage gives a PWR bonus for Melee and Ranged damage calculations as well as increasing the power of Force's Elemental Conversion, regardless of if the element matches the enemy weakness.
For example, you have a Sword with 1000 MEL-Pwr; if it has 25% element, it has 1250 MEL-Pwr for calculations, and if it has 50% it has 1500 MEL-Pwr. For Force, a 25% Rod would give a 12.5% damage multiplier with Elemental Conversion, and a 50% would give a 25% damage multiplier, assuming you are using a Tech that matches the Rod's element.