Trial and error. My best advice is knowing when to pay attention and understanding conditions.
"Thinner" air (high air temperature, high humidity, high altitude) has less O2 (oxygen) per volume and requires LESS fuel.
"Thicker" air (cold air temperature, low humidity, low altitude) has more O2 per volume and requires MORE fuel.
Since I commute to work most of the time, deciphering jetting is pretty easy. If my bike runs much better on cooler, less humid mornings that it does than on a hot and humid afternoon, it tells me that my bike could be running richer than needed.
I also pay attention to what part of the power band (basically the rpm range) is running rich or lean for a given condition. Does it flatten out on top (high RPMs) more when it's hot and sticky or when it's cool? If so, it's rich at the top end and a smaller main jet might be worth a try. It seems weaker off the low end in cold weather than in hot weather? Maybe try a larger pilot jet.
During the process, change one thing at a time. I always work with either the main jet or the pilot jet based on the seat of the pants data I get over a given time period (a couple of days at least for me.) I want to ride in different weather as much as I can. The coolest time of day versus the muggiest times over the course of a week or two will tell you a lot about how your bike is really running.
Rull of thumb on here is more flow needs more fuel. But that doesn't replace testing. Most pod filters are MORE restrictive than a stock airbox. Don't trust a rule of thumb, test them.
Another rule of thumb is to go to the point where things a bit too lean and go just above that. I believe in that rule and I test against it.
One rule of thumb on here is that if you get backfires, your too lean. It was the opposite for me. I'm slightly leaner than most on here and my deceleration backfires* are nearly non-existent. You need to test this stuff for yourself.
* Don't jet for this though. Jet for performance. Decel crackle and pops are cool. If you get them with good performance it's a good thing!!