Hi,
The Leopard Gecko generally experiences eye problems as a secondary infection to an initial infection. From the information that you have provided in your post, it sounds as if this is what is taking place with your leo.
Dusty environments lead to bacterial conjunctivitis and it sounds like this may be what your Leo has. He will need the medications that the vet has presccribed in order to recover.
You should also clean his cage thoroughly and change the substrate in it that you are currently using to prevent this from happening again. Paper towels and Newspapers are the best choice for this as they don't create dust particles that can infect the eye.
While there are many substrate products available for purchase, they can become harmful (sand, vermiculite, calci sand, ie.). Each of these products contain particles that if ingested can cause blockage in the digestive track.
If this information has been helpful to you then please do ACCEPT. Positive feedback is also appreciated. Let me know if I can help you with this further.
Good Luck, I sincerely hope that all works out for your little guy!