I suppose it depends on the calculator, but, I don't really see it as a problem. The calculator that I normally use doesn't have an option to use vg/pg nic base, just either pg, or vg. So, if your calculator is the same, you'd have to do some manual calculations if you wanted to accurately figure the end resulting pg/vg ratio. However, if you're like me, and don't mind if it's off a little bit, then it would be no problem.
You will have to take into account that the nicotine strength will be diluted with every drop of flavoring added. I did a basic calculation on the calculator, and you can get it to 10mg nic-strength, as long as you didn't go above 8% flavoring. That's just an example, and something to think about when figuring out what nic-strength/flavor % ratio you want.
If the end PG/VG result really doesn't matter, I would do all of the calculating as if you were working with 100% either VG or PG.
Edit: If the end PG/VG result does indeed matter, I would search for a calculator that allows you to enter a pg/vg nic base.