I had always played with the finger pads (kind of like, I'd lay my index finger across the frets and do my runs, hammerons/pulloffs off it in a kind of sweep pick way because i'd always be in the pentatonic... and that's how I was playing my single picked scales too). I'm still going to keep that technique when playing blues or 'real' rock (haha) but if i'm getting into the fast alt picked scales or whatnot, I've got to switch my hand to playing with the fingertips and learning that fact makes me feel GREAT.
I should've known, after so many years learning the stupid violin.. but there's always a proper way of playing something and eventually it'll come to you through the natural learning process.