Depends on your brewing method. The package is assuming that you're doing an all grain recipe and you have a rough idea for what your usual boil off is in your boil kettle. No top off water is usually necessary with this style of brewing. But, you're doing a kit and using makeup water after the boil to get to your final volume.
This is fine and here's how i'd do it:
Add the amount recommended for your final batch size (say five gallons) and don't worry about adding it to your makeup water. The reason is, when your wort boils, it's just the H2O that's boiling off and not the salts and minerals that you've put into the water. Those stay behind in your remaining liquid and wort. So, when you top off with water, it will dilute back to the concentration where it should be for five gallons.
I would also top off with distilled water to avoid adding additional minerals back to the final batch.
