I've never bothered boiling the top-off water. Furthermore, boiling removes oxygen from the water. Yeast need that oxygen, so if you do boil the top-off water it's a good idea to aerate it, either before or after mixing it in with the wort. Easiest way to do that is to dump the water into the wort in a rough manner--not gently. Or, a funnel can be effective too. However, it could be argued that this process cancels the sterilization benefit of boiling the water to begin with. Hence, I don't bother and use water straight from the tap.