There are many causes for eye discharge. Some people here have had luck fighting the boogies by switching foods or sources of water. A few people have had good results with bottled distilled water for babies.
Max doesn't have staining eye boogies, but Teddy does, so I am looking for a solution too. I have used happytails eye pads in the past and they helped. Need to order those again.
In general, keep the area clean and dry as possible. The dark stains are yeast and yeast thrives on moisture.