Typically, yes, you would check them each with a clear tube. The bike has to be perfectly level on the centerstand so the left and right inner carbs can be measured up against the outer carb lips.
But if a bowl drain is broke, it's not easy. You can try swapping bowls temporarily, but often the gasket may not match up etc. If you put in all four new fuel valves and all of the floats are matched up, as I describe on the website, that will likely be good enough. You can re-visit the fuel level if the jetting seems off on the one or two inner carbs based on the plugs.