millis() gives me the current time that my program had been running, if my program is running for more than 90 seconds, I will never be able to execute my 90 second countdown timer consistently.
That you have such silly ideas demonstrates that you don't understand the basic examples yet.
You need to understand those FIRST, before you start to modify a program full of irrelevant code. Your stubborn approach is holding you back.
Take a few minutes to study, download, run, modify and understand the "blink without delay" example, linked in reply #5.