So I've read that the time is calculated from the pattern of Bowsers hammer throws in 8-4 for any%.
I'm confused when to start my timer and I want to submit a run from Switch Virtual console. Anyone know when I should start the timer or does it even matter?

Timer offset aka starting in the negatives helps people but you can start with a time of 0 as well as far as I know there will be more answers later on. Timing starts on the first frame in the first level.

The timer is purely for your own purposes (and your viewers', if you're streaming runs) to get an idea of how far ahead or behind you are. The moderators verifying your runs retime them regardless so however scuffed your timer is doesn't matter for verification purposes.