Jetting is finding the correct main jet to use inside your carb so your engine runs great. The wrong jetting can lead to a burned up top-end.
You probably know that an engine must have the correct mixture of air, fuel and spark to run properly. Air and fuel are the variables that change the most. They're also the easiest to adjust, if you need to, by rejetting.
So if you change something on your motor that alters either of these variables.....like installing a new pipe, removing airbox lid, etc....then you need to determine which main jet size is now needed.
Both the new aftermarket pipe and/or airbox removal examples from above will allow more airflow. So to get the air & fuel mixture back into balance, you know you'll need a larger main jet for your carb to allow more fuel to flow. Jetting, in this case, would be the process of finding which main jet size will give you optimal engine perfomance.
There are two more variables you'll need to think about:
Temperature = changes in temperature will change the density of air. So if your quad ran great in the summer and it runs like chit now, you'll likely need to increase the main jet a size or two for winter
Elevation = change in elevation will effect air flow, again because of density. The higher up you are, the thinner the air is. Thinner air means more flow. The rule of thumb is you go up one main jet size for every 2000 ft of elevation.
Good luck!