carb setup

Currently have my carbs off, 

just wondering Should I balance them first when i put them back on or adjust the mix screws? or does it really matter, logical route seems to balance them with the air screw all the way in.

cheers.

Set up the pilot screws to the recommended setting to begin with. Screwed right in the engine won't idle so you're giving yourself problems before you begin.
Balancing the carbs has nothing to do with the jetting, all it does is make sure that the butterflies are allowing the same amount of air into each cylinder, so one cylinder isn't carrying the others.
This is most noticable at low revs and idle.
When the carbs are balanced, you set the idle speed using the throttle stop screw (the one with the big yellow knob) making sure that the throttle cables have free play, so they are not affecting the idle speed.
If you have still got a rough idle at this point, then you can adjust the pilot screws a little at a time to try to smooth it out.
Bear in mind that a lot of factors can cause a rough idle, plugs, valve clearances, loose exhaust joints, etc. But of course you would have done all these before trying to balance the carbs wouldn't you!
I might add that in all my time I have only had to adjust the pilot screws once from the factory settings on a standard bike, and that was due to worn pilot screws. To put your minds at rest it wasn't on a modern bike like these 

When I have the carbs off I feel it would be best to adjust them as per the haynes when i balance,  get everything spick and span, unfortunately i do have a leaky exhaust at the headers but that has to stay that way for another month or so until I can afford stainless downpipes.