You should use the calculator. If you do that, you wont end up w/ too much sparge water - you'll know exactly how much you are going to have before you start to brew.
If you do a longer boil, just make sure that you add the hops at the right time. For instance, if you do a 90 minute boil, your first hop addition will likely be at 60 minutes. So you will boil for 1/2 an hour, then begin your hop additions.
As far as I know, a longer boil will not effect the flavor.