Alternate Picking Quest

Hello there,

I'm new to GMC and this place seems pretty cool so far.
I have watched quiet a few of the beginner videos and am working on just doing scales and a lot of the basic stuff to help improve my accuracy and speed before I get into songs I would like to do.

My question is kind of easy and hard to explain at the same time.

Lets say on a scale there are three notes I have to hit, for example Open E (down), 1st fret (up), 3rd fret (down), and then I have to the A string. Would I go down again, or would I go up.

What my real question is, do you ALWAYS have to go up then down when you are practicing scales, or are you looking to go whats the fastest way to get to the next string and strum? Sorry for such a long explanation, it was kind of hard to explain.

All help is much appreciated.