I shall keep reading because it is not clear to me what makes it "tick" to jump out and continue.
Yup, they can be confusing at times. You may have this part figured out but we will start someplace.

Once the timer is setup it will run in the background as if there is a second chip. This second process can be looked at as an alarm clock. When the alarm goes off, timer overflows, it will interrupt the main process.

At this time we turn the alarm off, disable the timer, and do whatever... get up go about our day....

Then the alarm is set again...