I have been doing full boils (6.5 to 7 gallons pre-boil in the kettle) using kits that specify a partial boil. I had been just using the hops as indicated in the kits and I found that the results were always on the bitter side. They didn't cause the beer to become bad or anything, just more bitter than I liked. This was especially true of the kolsch kits from brewer's best. It is supposed to be a lighter beer, but the bitterness was a bit strong.
As an experiment, I brewed up a kolsch 2 days ago from the brewer's best kit and instead of a 60 minute boil I reduced it to 50 minutes. I am hoping for a slightly reduced bitterness. I intend to keep messing with the timing until I get the bitterness where I like it.
Its up to you. If your beer is too bitter for your taste, add it later or add less. You have 'settlement authority' in this matter.
I will be honest and say that I can't equate a bitterness level with the IBUs spit out by the calculators. While I can tell bitter from not bitter, I just don't have the background to understand how a calculated decrease of 'X IBUs' impacts a beer. So for me, using the online calculators isn't a useful option. I'll have to use trial and error to find the proper bittering levels.
It could be worse.