I am a little lost on this. If the app deadline is Oct 1st, does it mean I should submit by 9/30th 11:59PM or Oct. 1, 11:59PM?
11:59 PM September 30th.
depends on teh Uni.
As an example, Berkeley clearly says, 8:59 pm local time, on the day stated. In your hypo: October 1 before 9 pm PT.
Usually they mean by the end of the day on the deadline. So if the deadline is October 1, then you typically have until the end of the day (11:59 pm) on October 1 to submit.