the longer fish are in the bag, the more ammonia is building up. during this process, the pH in the bag is decreasing slightly as the nitrogen equillibrium yields nitric acid. the decreasing pH is a not a bad thing, since ammonia is less toxic at lower pH.
when you add water to the bag from your tank or tap, you will very likely be increasing the pH in the bag. this will elevate the pH and result in higher ammonia toxicity. many fish are lost in the acclimation process, having suffered toxic shock syndrome (damaged gill filaments), and die shortly after or within a few days after installing in your tank.
if the bag is lightly packed (one fish per bag for example) and if the transport to your home is short (half hour for example) the change in chemistry is not significant. you can thus simply equillibrate the temperature of the water in bag and tank, net the fish and install them in your tank.
if the transition from store to home is a few hours or longer, chemistry equillibrium becomes more important. in this situation i recommend the use of ammonia resins (ammo-lock for example) to insure the prevention of toxic shock while acclimating the fish.
here's what i do. remove the fish with the water and place in a small bucket. add ammo-lock. gradually add tank water at a volume which represents about 20% (1/5th) of the initial volume. repeat the addition of tank water every 15 minutes until the volume in the bucket is doubled. for you math challenged, this takes an hour (you've already added the first 20 percent). then i pour off half the water in the bucket and refill with tank water. after another 15 minutes i pour ALL the water in the bucket through a net, catching the fish in the process, and then installing them in the tank.
turn off tank lights during the process.
always request only one fish per bag when buying multiple fish at your LFS, regardless of trip length. in addition to the ammonia buildup potential, in the confines of the bag, multiple fish can cause damaged scales and torn fins due to the tight space.
i'm not suggesting that my method is the only correct one. the vast majority of the fish i purchase are shipped to me and spend a minimum of 24 hours (sometimes longer) in the bag. thus my perhaps overly cautious acclimation procedure. if you have another method which has worked for you in the past, by all means continue to use it. if on the other hand you've had problems with acclimation in the past, give my method a try.