Highest stack in auton?

Is there a seperate highest stack for autonomous? Thanks!

Assuming you mean “seperate” as in if highest stack is counted in autonomous, yes, highest stack bonuses are calculated into each team’s score. But, these bonuses are also recalculated at the end of the match

To explain it more clearly - highest stack bonus is applied when counting the intermediate score at the end of 15s autonomous period. This intermediate score is used to decide the auton winner and awarding 10 bonus points, but the score is otherwise meaningless.
Highest stacks, as well as all other points are reevaluated at the end of the match to form the real final match score.