I am practicing major scales on guitar(2 notes per string). Going from String Low E to high E, I move my pick downward for 1st note and upward for 2nd note of the string. My question is what should be the direction(upward/downward) of the pick when I play the scales reverse(from String High E to Low E) ?
This is something you really need to sort out for yourself. There are going to be anomalies in picking direction at some point in whatever anyone chooses to play. There will be times when the well revered alternate pick routine just needs to be changed, albeit for one stroke.
Part of the fun of learning something is to find your own way, rather than be guided by others. This is one such instance. Try alternatives, and if it works for you, stick with it.
In many beginning techniques the student is taught to keep a steady down - up pattern with the pick, to develop the muscle memory of the regular rhythm. Phrases should always start with a down pick.
To work on this, you should keep playing whatever the next direction of the pick is until you end the phrase, no double picking even on string changes (no up-ups or down-downs).
When starting the scale again on the high E, you should start with a down pick and continue the down-up pattern to the end.
EDIT: for more clarity.
The technique work I'm describing works rhythmic muscle memory of the down - up motion, specifically to build a regular motion and avoid attempts to double down or double up.
You can go up the strings with an up - down pattern as long as you keep the rhythm steady and don't double pick. You can also work just up-down, the point is to have each pick stroke alternate.
Eventually players will be able to choose whether to switch to up or down picking in a certain passage.
Practise it down up strokes Practise it up down strokes Then practise it starting on each of your four LH fingers. There will be different numbers of notes on the strings. Then you'll be ready for anything.