You wanna get it to the the 'T' that allows each tappet (exhaust and intake) to have free play. It will barely be enough to see, but you can feel it lift. They should both be lifting. That's top dead center of the compression stroke, so that the valves are completely closed and the tappets free to adjust.
There are conflicting marks on the flywheel sometimes, but choose the mark that:
A ) leaves both tappets free to move the little bit they do
B ) raises a soft object (I prefer a straw) to its peak in travel if you've removed the sparkplug and sat the straw on top of the piston.
Both tappets being mobile means you're in either the compression or ignition stroke, but not necessarily the perfect moment. The peak of your straw (or whatever you use) is that perfect moment: top-dead-center during the compression stroke, very immediately before ignition. Remember to have the spark plug out or the compression will make it hard to line up perfectly.
In addition, your cam sprocket has a groove in it that should be pointing almost perfectly up at the "notch" in the head casting above it. It's an additional method to be sure, but more related to cam timing than valve clearances. If you have A and B but the cam is off for some reason, it's most likely that the cam chain has skipped a link or two due to improper tension or installation, rendering the bike very likely unable to run.
In short, adjust both valves with the flywheel in the same spot. That spot needs to allow both tappets to move, meaning both valves are sealed by their springs, not the rockers/tappets/followers. Lotta names for it, but it's the arms that push the valves into opening.
If your bike is from 2000 or earlier, the cam chain requires manual adjusting which means it can also give you the "clackety" noise when it's really not tight enough. Even easier to adjust it than the valves, but I'd say if you did the valves as you described, that could be a part of it. Remember to leave more clearance than less as the clearance will grow tighter over time. Valves "seat" themselves like that.
Also, I commend you for learning this instead of leaving it up to some mechanic who might not put an ounce of passion into the work. You're becoming a surgeon.