If it causes any staining, go to Home Depot and buy a small container of Iron Out. It's white, with red cap and label. It really works well, just be careful, it's pretty nasty stuff.
I worked for a well company, we used it, and customers noticed near-instant results. It worked on my rust-stained t-shirts, too, when nothing else would.
To chlorinate a well, dump a couple gallons of regular (no scented stuff) chlorine bleach down the well.You will have to remove the cover to the well to do this. Use 3 gallons if your well is more than 350 feet deep, and 4 if it's over 500 feet deep.
Run a faucet in the house untill you smell bleach. Repeat for each faucet. Once you have a chlorine smell at each faucet, let is sit for a couple hours, preferrably overnight. It wouldn't hurt to dump another gallon down the well at this point.
In the morning, thoroughly flush each faucet. also flush the well thoroughly, running it out the garden hose for a while, but try to keep the water off the grass or any gardens, it's not so good for them.
Like someone else suggested, it wouldn't hurt to flush your water heater once a year, but for different reasons.