How to Determine Which Jetting Circuit or Jet to Adjust

The image below illustrates which metering circuits govern each throttle stage. For instance, if you are having an issue in your top end of the throttle between 3/4 to WOT (4/4) you need to address the main jet.
This is a simple diagram to tuning your bike and applies to CV carbs and mechanical carbs found on your Honda Shadow.

When tuning you want to begin with your idle, which is when your throttle is not being touched. 
Once the bike idles properly, move on to the idle to 1/4 throttle throttle stage. That is -  when your throttle is at idle and rolled back 1/4 of its range of movement.  

Honda Shadow Keihin Carburetor Tuning Diagram