I couldn't find anything on Eclipse 2, but found Eclipse 3 here
. Is this what you are talking about? Unfortunately, I cannot find an MSDS or ingredients list for this product, but they refer to it as a "mineral system" and that usually means something copper based to prevent algae and silver based to prevent bacteria. Chlorine is still required, though can be used at lower levels.
They say you add 20 ounces initially and then 1-1/4 ounce weekly -- both amounts are per 10,000 gallons. The dosage, if product is pure, is around 14 ppm.
I would guess that if this is what you used, then the copper killed the algae, but that there was too much put into the pool and/or the pH of the pool went up and you have now precipitated copper carbonate. You can have your pool tested for metals to see if you've got copper in the pool and if so, then that's probably what happened.
To remove the stains, you'll need to lower the pH, and use a metal treatment (sequestrant). You may also need to use ascorbic acid on the stains directly, though that's usually mostly needed for iron stains and if you do this you'll need to lower your chlorine level -- so I suggest using PolyQuat 60 algaecide since that will protect your pool from algae and will help lower the chlorine level.
describes the metal removal procedure in more detail.
The moral of this story should be: don't use copper-based algaecides in your pool. There are some that are chelated to help prevent staining, but it's usually just too darn hard to control the levels and, most importantly, chlorine alone can prevent algae (but it has to be relative to the Cyanuric Acid, CYA level).