Fish question, please help?!?

My fish has popeye, he's a Cichlid and him and my female just had babies, it was only about 2 1/2 weeks ago, so they're not very big, and I'm scared to just use the vacuum to clean the gravel. I have been changing the water out, but it hasn't been doing anything to change the nitrite levels, etc. Does anyone have any advice on how to take care of this problem? Without damaging the babies or mom, because they are doing fine. I moved him to a different clean tank for now... But just don't know what else to do.