The Purple Stuff will work fine and so will just about any other sequestering agent. I personally have had good results with Proteam's Metal Magic and Natural Chemisty's Metal Free in addition to the Jack's Magic line of products.
The first thing to do is have your water tested for metals (copper and iron) and then post a full set of test results!
You can test the stained area with a vitamin c tablet (or several in a sock tied to your pole if it is too deep to get to otheriwise) and see if the stain disappears or lightens. Next try some dry acid (ph down, sodium bisufate) in a sock held against the stained area for 15-20 minutes and see if it disappears or lightens. Third (this is a bit complicated), take a small plastic container such as tupperware and fill it with rock or sand and water and snap on the lid so it will sink and sit on the stained area, next take an ordinary kitchen sponge and tie it to the container with string or rubber bands and soak the sponge with sequsterant. Place on the stain and let it sit for 5 minutes.if the stain does not disappear resoak the sponge and let it sit on the stain for 15 minutes, if the stain does not disappear then resoak the sponge and let it sit on the stain for 30 minutes.
If all of the above fail put a trichlor tab in a sock and hold it on the stain for about 15 mintes.
Post your results of these stain tests back here along with a full set of test results including metal tests and we can take it from there!
Also, what color are the stains? Brownish can indicate iron, grey to black can be manganese, blue or black can be copper, white to tan can be scale, and black can be algae (these are the stains most commonly seen).