Whatever you end up at post-boil, top off to whatever your recipe calls for in the fermenter (e.g. 5 gallons).
If this is for extract (with or without specialty/steeping grains), assume whatever Beersmith or another program predicts for the OG; don't trust your hydrometer. As long as the batch size and ingredients are correct, you can't really miss the OG. However, if you measure it yourself, you might think you're off because it is very difficult to completely mix the boiled wort and top-off water. So, putting the hydrometer in and adding water till you get the SG you want won't work.
When it comes to gravity, it doesn't matter how big or small your boil size was, as long as you top off with whatever you need to post-boil to end up with the correct batch size (e.g. 5 gallons).
However, as mentioned above, the density of the boil does affect hop utilization. An easy fix is that if you're doing a partial boil, only boil part of your extract and add the rest immediately after the boil (and let sit for 5-10 minutes to pasteurize).
An even easier thing is to use Beersmith or a similar program and input your batch size, boil size, extract to be boiled, extract post-boil, specialty grains, and hops; and see what your IBUs end up at. IBUs can be changed by varying the boil density (amount of extract/grains added pre-boil and boil size) and/or amount of hops (along with their type, boil time, etc.).