The right way to do something is the way that's right for you.

I've just checked, and I find I use the pick both ways, according to what instrument I'm playing (eg single course of strings like a 6 string guitar, or double courses like a mandolin), what kind of music and which pick I'm using, and whether I'm picking out notes or strumming or whatever, and whether it's just me, or if there's a group of musicians.