If there is a paint dot...yes, it is to show the light spot of the tire. Some have it, some don't.
That said, I have seen many a wheel whose valve stem area was NOT the heavy spot of the wheel, with or without tubes. Simply lining up the paint dot with the valve stem does not guarantee the best outcome.
Removing the tire itself, then putting the rim (and tube?) on the balancer will reveal the true heavy spot of the assembly without tire.
As long as you're adding weight in only one general area, there's really no such thing as too much weight, though it might be a problematic fit and/or ugly.
All the best,
Shane