please explain where i've confused you? because someone else could feel the same way.
i'll try and double guess where you are going with this though.
first of all don't forget that you have the sidecover off so the mark through the hole is completely and utterly out of the window.
you are looking at a flywheel with a long bolt in the top hole vacated by the sidecover screw. you now need a teardrop to put on the bolt and for it to run really close to your protractor. that's why you are best having two nuts on the bolt sandwiching the teardrop. you bring it right in close to the protractor and lock it facing the middle of the flywheel.
with the protractor being blue-tac mounted you keep spinning the flywheel to a dead stop either way and adjusting your protractor and squidging (yes this is a technical term used by the works spagforth blue thunderflash team) it around till say it starts and stops say 25d before and 25d after TDC.
then where the protractor says 0/360 degrees is your TDC. this is then marked on the flywheel and painted (IMHO) to make it clearer for the timing light. undo everything, cover back on.
hope this helps and as i say, let me know if i've been a little ambiguous somewhere.
regards
Taffy