Seeing as how i'm yet to get the jetting right on my bike, i might not be the best to talk to, and most likely you won't get the jets just right on the first try as it is a trial and error process...
hopefully you can read that... basically what it says is that the different circuits overlap some for the carb. keep in mind that isn't our exact carb, per say, but it is just for an idea. at most places there are two circuits in use at a time, but at the extreme ends (fully open and idle) only one is in use. so yeah, jets affect each other, and you can sometimes compensate one jet for another, but since the idle and main are at entirely opposite ends of the spectrum, they won't really do that.
and trust me when i say you can spend days on this site learning about jetting, and freaking weeks actually doing it.
www.mikuni.com/pdf/hs40_manual.pdf i printed this out and read it. again, it is not our carb, but the tuning should be almost identical. some people suggest different ways of tuning it than what that manual says, so don't take it as the one and only way of doing things. i'm sure other people will agree, the only REAL way of getting jets EXACTLY right, would be running your bike on a specific throttle circuit for 15-20 minutes, killing the bike at that instant on the side of the road, and looking at what the spark plug tells you (generally that light is lean and dark is rich) but even then, the precise coloration of the perfect running spark plug is not known to me...
read the forum, read the manual, give it a shot, and feel free to come back for advice. hopefully someone with a bit more experience than me will chime in here with a few pearls of wisdom....