It depends on what you brewed to begin with.
If you made a 5 gallon recipie and only boiled 3 gallons then you need to top up to 5 gallons to get you recipie SG. You can add boiled, aerated water to the fermenter.
If you boiled 5 gallons of a 5 gallon recipie, then you can add make up water to the boil or to the fermenter if it is boiled and aerated.
Some have added water to the fermenter without boiling at all (myself included) without any adverse effects. It depends on how well you trust your local water.
Keeping your water topped up in a 5 gallon boil helps with your hop calculations IMO.
How do you BBQ an elephant....first you get your elephant....