Normally you shouldn't need plumber's putty anywhere.
Normally, the new rubber grommet that comes with the new flush valve will seal against the bottom of the toilet well. If you tighten the plastic nut, it will pull the fill valve down and the rubber grommet will create a water tight seal at the base of the fill valve.
What often happens is that if you have a plastic tube (called a "flexitube") between the water shut off valve and the fill valve, then when you replace the fill valve, the plastic end of the flexitube won't conform to the new fill valve right away, and it'll leak.
You can generally solve that problem by replacing that plastic tube with one of those braided stainless steel supply hoses. They cost about 7 or 8 dollars, but they work well and are re-usable many times over.
Exactly where is the water leaking from?
Last edited by Nestor_Kelebay; 09-09-2009 at 08:45 PM.