I notice when I play a 3 note per string scale ascending and descending using alternate picking, I use economy picking to change strings, so going up a scale im always moving downwards to the next string, and vice versa. Anyways, is it a bad habit or should I just continue on?
Economy Picking is good!
It's probably better to practice this way that it is to practise strict alt. picking
I say do whatever feels more comfortable and if it makes you play faster then I cant see how thats a bad thing
It doesn't matter - practice whatever picking style you want to, the scale you're using is pretty much irrelevant becase in reality you're hardly ever going to use those kind of straight scale runs.
Actually called Mark!

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Yes. I'm completely aware of that. I just wanted to know because this was more comfortable for me than going strictly alternate.