Accidently drained my pool this year. Now looking at refililng 35K gallon gunite pool with well water. Water runs through softener but, still allows some iron to bleed through.

I have some old iron stains on the sides and floor that i want to get rid of. Should I hold off on refilling and attack them while it's empty? Is that easier?

Also, what do i do to ensure that the stains don't come back with the new well water I'm adding?

I have algicide, 5lbs of vitamin C, plus 4 quarts of mineral magnet that i saved from last year when i was going to try and remove the stains.

Thanks for the guidance