The process you'd want to follow is something like this:

1. Remove the stains with Iron Out; pump out the rinse water from this process.
2. Begin filling but do NOT allow the fill water to directly touch the pool walls. For example, put the hose inside a bucket, and put the bucket in the pool.
3. Begin adding the Mineral Magnet but only if the image below is the product you have

Add 1 cup to the bucket BEFORE you begin filling, and then add another cup every 4 inches of water, till you've added a quart.
4. Begin operating your pump and filter as soon as you can, but do NOT let the water from one of the returns splash directly onto a pool surface.
5. Keep the pH low; if it starts to get above 7.4, add acid. If the pH is TOO low (below your test kit color) add borax, 1/4 box at at time, to your fill bucket. Do NOT dump it directly on the pool surface.

Before I can tell you more, you need to put COMPLETE pool info -- pump & filter make, model, & size; pool equipment if any, gallons, etc -- into your PoolForum signature

One more thing: if you *really* want to avoid staining, pre-filtering the water will help. I checked on Amazon, and it's possible to put together a pretty substantial pre-filter system for around $100 using a couple of Culligan pipe line filters + some trichlor tabs. If you're interested, I'll list out all the parts for you. You'd have to assemble it yourself, and pick up some 3/4" PVC and 1" PVC adapters locally. You'd need to be able to use Teflon tape or Teflon pipe dope, plus Channellock pliers. It would be resusable -- and in fact, if you make it, you should use it each time you add water to the pool.