You can brush the pool -- but what you are waiting for, is to see the stains disappear. If they aren't gone in a few hours, add more ascorbic acid directly to the stained areas. You can also go ahead and add a single dose of HEDP. That way, the HEDP will 'grab' the metals once the ascorbic acid 'releases' them. If you have a CuLator, you can put it into the skimmer at this time.

Once the stains are gone, add the HEDP, give it time to mix, re-install your cartridge and begin slowly re-chlorinating your pool. Continue to use the polyquat till you've established a good chlorine residual.