What RG said about trimming the front derailleur (left shifter). Also, while standing next to or straddling the bike, look down at the derailleur while clicking the shifter one click at a time. Note which way it moves. When you shift the rear (right) shifter to smaller numbers, the chain moves inward (onto bigger cogs). And vice-versa.
This movement changes the angle at which the chain moves through the front derailleur. By understanding which direction the front derailleur moves (inward, outward) when you turn the left shifter, you can understand which direction it needs to be trimmed if it's rubbing after a shift of the rear.
Also, you should take your new bike in for its 30-day tuneup. As new cables seat themselves and settle in during the break-in period, they can seem to "stretch" and require adjustment. Have the shop show you how to do this for yourself, too.
As you gain more experience, you'll focus less and less on the index numbers on the shifters until you find you never look at them at all. You'll shift by feel, and you'll tim the FD without even thinking about it.
RichC
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Training: 2002 Fuji Roubaix Pro (105 triple)
Commuting/Daytripping: 2001 Airborne Carpe Diem (Ultegra/XTR, touring wheels)
Commuting/Touring: 2000 Novara Randonee (Sora/Tiagra/LX, fenders, lights)