Brianhuynh05, this will take us down a bit of a hole as we are now getting into the main principals of TFP on how to maintain a pool. Reading in pool school will help you understand a bit better.
In short by bringing your chlorine up to the required level and keeping it there the stains should fade over time. If you want to try to get them to disappear faster you could raise your chlorine level up to SLAM level and still be safe to swim.
In order to determine the target value of chlorine we will need to know the CYA level of your water. Once you have your CYA level we would want to look at the Chlorine / CYA chart in Pool School
HERE to identify your SLAM level.
For sake of conversation lets say your CYA is 50, this means that you should never let you chlorine be lower then 4 ppm but should try to maintain a chlorine level between 6 - 8 ppm. With a CYA of 50 your SLAM level will be 20 ppm, please note that a SLAM is normally used for sanitizing your pool for one reason or another. Most people use SLAM when experiencing an algae outbreak after opening or find themselves here after searching the internet after being feed up with the pool store.
In order to determine how much chlorine to add (we recommend bleach or liquid pool chlorine) you would use the PoolMath link and fill in the size of your pool, your current level of chlorine (3) and then enter 20 in the goal field and it will tell you how much to add. For example if your pool is 20,000 gallons with a chlorine level of 3 you would need to add 5.5 gallons of standard bleach or 3.4 gallons of 10% liquid pool chlorine which can be found in Walmart, Lowes, and others. Please note that many people are having difficulty finding bleach or pool chlorine in sufficient quantities at this time.
It is safe to swim in the pool with chlorine up to 20 ppm based off a CYA of 50.
Now that you have your chlorine level elevated you will want to keep it there by frequently testing and adding the required amount of bleach to bring your level back up to 20 until you are satisfied with the appearance of the stains.
This is where your test kit comes into play. Most test kits can only measure chlorine up to 10 ppm. As a result we recommend you get one of the recommended test kits,
HERE is a link that compares the recommended test kits.
Hopefully this is helpful, please feel free to ask any other questions you have.
