Funny...I just did this mod...and when I pulled up the co numbers on the screen .. both c1 and c2 were set to 0 (zero). I recently obtained the bike in a trade, so I just adjusted the numbers to have a 10 digit difference..c1 being lower. Bike isn't running as rough now, lol.My experience only comes from reading the original thread many times (http://www.600riders.com/forum/fz6-mods/4809-dyno-tune-co-adjustment-leo-vince.html)
Basically, yes higher numbers mean more fuel, lower/negative numbers mean less.
Yes, you should decrease both numbers equally, C1 are the cylinder 1 and 4, C2 are cylinder 2 and 3.
It is normal for C2 to have a higher number, the inner cylinders are richer to control temperature (a lot of EU bikes have something close to C1:-3 C2:16) try to maintain the relation between C1 and C2 that your bike had originally.
Watch out, people who have grounded to the battery have apparently had problems with both values resetting to zero, which is not good.