Hi Parker,
Regarding Skimmer, just follow directions- I believe you keep it on. Don’t alter what directions say just cause you think it’s good.
I didn’t realize you have a reefmat like I do. Not only did I keep it on, but I increased the inches on the auto-advance to 1.0- 1.3 inches. I ran through a whole roll as it was picking up all the GHA.
I recommend you do a big manual removal of GHA and then do 20% water change right before you add Flux. Don’t worry about nitrates/phoshates during treatment. As long as you are diligently removing the die-off of GHA (grey stuff still on rocks/sand and the loose stuff floating in water, you’ll be ok on parameters.
The GHA doesn’t go anywhere unless you remove it.
Regarding amount of Flux to use; you and I are basically the same in total water volume and rock/ sand. Close enough. I used the entire bottle of powder except for a smidge. Since you are using capsules that you have to take the powder out of, I would use the all and on the last one, use 75%. But to be honest, I don’t think it will hurt to use it all. The directions will say if it’s a no no.
You won’t really have “extra” and if you did cause your tank was smaller, you Would NOT use extra.