You should add the initial sequestrant dose right after the aa treatment has lifted all the stains as directed in the article.
Then follow the instructions on your particular sequestrant for maintenance dose’s & frequency.
Without replenishing sequestrant the metals will eventually redeposit onto the surfaces & another aa treatment will need to be performed again.
The only way to stop the cycle is to drain the sequestered water & replace it with metal free water. Or do the slam/polyfill thing to get as much out as possible.
If your iron content is quite high You may need to do all the things - slam/polyfill then aa /sequestrant , then replace some water & keep with sequestrant for insurance.
If the iron level is quite high there’s only so much a sequestrant can do (no matter how expensive it is).
About your landscaping rocks- the pool deck should be designed to drain water away from the pool, if the rock’s placement is impeding that or causing the water to run into the pool that needs to be corrected (no matter what the rocks are made of).