It's kinda confusing.
Here's how the Honda shop manual describes it:
"Rotate the crankshaft clockwise and align the "1.4T" mark with the index mark. Make sure the #1 piston is at TDC of the compression stroke.
(both of the rocker arms on 1 should have free play, as in on the low egg-curve of the cam lumps, instead of the pointier rises. You should be able to wiggle both freely.)
At that point, you measure the valve clearance for the valves by putting the feeler gauge between the camshaft and the rocker arm 'slippers'.
Honda's manual says 0.05mm(0.002 in) on the intake and 0.08mm (0.003in) on the exhaust.
Hondaman suggests 0.05mm (0.002 in) on the intake, and 0.005in on the exhaust for valve longevity.
With Cyl. 1 at TDC compression, you check IN and EX on 1, then the EX on 2, and the IN on 3.
Adjust so there's just a little drag on your feeler gauge, then double check with the next size up- make sure it won't go in. Go-nogo gauging.
Torque that lock nut down to 9-12 ft-lb, according to the honda manual, (this is where that little tool comes in REAL handy, otherwise that adjustment screw moves pretty easily.) Recheck just to make sure, because you just know the darn adjustment screw moved.
Rotate the crankshaft one full turn clockwise (the way the wheels go, for a mental picture). (here's your 360*)
Align the 1.4T mark with the index mark again. This time 4 should have the same play that 1 had on both the little rocker arms.
Check and adjust IN and EX on 4, then EX on 3 and IN on 2.
This is about verbatim out of the honda manual with my additions here and there. I can't pretend to be any kind of expert, I watched Paulages do mine, and related it to you the way I did so if I need to check my valves, I can come back and read it all in one place.
We've all gotta be newbies sometime, let's be newbies together, right?