The BEST way? Exhaust Gas Temperature guage and/or dyno. EGT guages work well in the field though too. They aren't cheap, but you can use them on more than one bike/sled over the years and really, a decent egt guage is cheaper than piston/bore.
Doing it by feel is very subjective and very experience dependent and will also be affected by plug look and piston wash.
There will always be some overlap between carb circuits. When I am really looking for all of what a particular engine will give me I will overjet the main and then find the pilot jet that will give me a solid steady idle with the air screw at exactly 1.5 turns out. I will then work up the circuits-looking for good response without affecting that idle.
I always mark the throttle lever/twistgrip to correspond to the actual throttle slide so that I am not guessing at throttle opening.
I will hold the bike/sled/seasled at 1/4 throttle for a good distance and feel/listen/look for surge or four stroking, then I will vary the throttle back and forth over that range I am trying to isolate, go back, look at the plug, and make changes accordingly then try it again with a fresh plug.
Only when that cicuit is good will I move on. Concentration on ONE circuit at a time is crucial.
I like the bottom up method because it is a lot easier to stay away from big throttle openings in start up/warm up and testing than it is to avoid idling and chopping the throttle while looking for the right main. If you have the idle good, it won't color or load up the plug to be at low throttle openings while trying to get the cutaway/neeedle/needle jet. The deliberately oversize main will keep the main from affecting the lower circuits.