believed fungal/bacterial infection

I noticed my 3 black ocellaris what seemed to be their tail fins receding in color, white bits at the end and they stopped eating, hiding all the time. Then one fish's port eye was expanding/bulging after some googling I determined this was likely popeye, so I began to dose Pimafix/Melafix, around 14hrs later the eye is going down and they ate today for the 1st time in a couple days (major stress relief for me, was sick with worry)

Question is: I changed the water before I started treatment, I have used this stuff before in a FW tank with amazing results, and again here in SW, tho I've read that they destroy the biological filter, so I want to change the water before I dose for the second day, will this decrease the effectiveness? I just want to make sure there is no chances of ammonia, and no one sells any of that fancy ammolock stuff around here.

Thanks