What's relevant is only that the numbers are in order and entered bottom to top. It will sync faster if 0 is at the top, and given that fact the reference tooth table can only look only one way with any particular primary trigger wheel.
Where the cam sync occurs is not really relevant unless it races with primary trigger events, in which case it needs to be manually adjusted or trigger edge changed (falling/rising) to offset it out of trouble.
What you always do is strobe the ignition to see where it's at, and if not near correct then shift the ignition output table for rough adjustments, finer steps are made with small adjustments to primary trigger settings - namely the "first trigger tooth" and "TDC after the trigger".
All this will be easier to comprehend later this year, development is geared towards having VemsTune change the way it presents the tables. The user is forced to input in a table which cylinder is using what outputs and table rows. The table does not serve any purpose for the firmware and how the engine runs, it is dedicated for the purpose of making it easier for the user to get the idea.