You've probably gotten confused by some of the answers. The most important thing that most of them are implying, but not explicitly saying, is to make sure that the bottom of your top bowl/pan/container does not touch the simmering water.
Check your level of water in the bottom pan using both pans while they're cold. You don't really need that much water - an inch will more than do it for melting chocolate and short additions to that. Using only the bottom pan, bring the water up to a boil. (With or without a lid but faster with a lid - then you won't use the lid anymore.) Turn your stove down low, so the water will only simmer. Put your top container on with the chocolate and start the melting process.
If all you need the double boiler for is to melt the chocolate, you can do that in the microwave. Just make sure you stir it often and cook in small time increments once it starts to melt.
my own experiences