Penetration has nothing to do with spell level - it applies after all that..
Start by generating the Casting Total (roll + Aura + Arts) or (roll + aura + Arts)/2 or (Aura + Arts)/5.
Subtract the Spell Level. (For a spont you can choose to restrict the spell level so you have some points left over.)(*)
That's that starting point for Pen. Now take the Pen Ability score, and multiply the Ability score (and nothing else) by 1 + any bonus for AC or Sympathetic connections.
Add the multiplied Pen Ability score to the excess points from Casting Total - Spell level, and you get the final Pen Total.
Pen Total = (Casting Total - Spell Level) + (Pen Ability Score * (1 + AC bonus + Sympathy bonuses))
[For a Device, the effect has a built-in Pen of 0, with no roll and no use pf anyone's Pen Ability. Thus for devices there is an additional option:- take the base Effect Level as calculated, and add a further +N levels for Pen. and get +2N Pen for the enchanted effect.
You do still always add the Aura Modifier - starting with the base of 0 or +2N, so in a Magic Aura you may have a +ve Pen, and in a Divine Aura -ve; but if the Target is, say, Infernal, it may be even worse affected and you may still zap it!
Device Pen = (0 + Aura) + 2(Pen. Effect Levels)
There is no core rule to devise a spell with enhanced (though House Rules might suggest it)
Wulfenbach is right to sya that Pen alone does not blow down Parma (nor any other MR). A spell or power or effect which challenges MR, will either penetrate and affect the target - and the target knows nothing (unless e.g. the flash of flames gives it away!);
or MR resists, no spell affects the target, and the target is made aware that they have resisted.
(And in this, MR 0 is specifically differnt from "no MR" - no MR means no resistance, no how, and no knowledge of resisted effects.
MR 0 can resist any effect with 0 or -ve Pen!)
After the effect has been resolved - the MR remains, unless special cases apply - such as a PeVi designed to dispell a specific kind of MR, which would be the thing to knock down Parma,
or perhaps ReVi to temporarily suppress if (compare ReVi GL to PeVi GL)