Dave

First of all, using ammonia is actually, chemically speaking, no help at all. Amines are ammonia without one of more hydrogen atoms. That is a simplistic statement though amines are actually a complex class of inorganic compounds, but the general statement is essentially accurate for this discussion.
First of all, one of the more common causes of fisheyes is a oil contaminant, followed by all sorts of other contaminants. Either way, if you are going to IMMEDIATELY add another layer onto the still-green layer, then treatment isn't appropriate. If any length of time goes by, then let the epoxy fully cure, and then wash with plenty of warm to hot water, using a green scrub pad and rinse thoroughly to remove all the dissolved amines on the surface. I know...the ads say blushless. Stick your nose near the hardener and take a careful sniff. Smell like ammonia? A small part of the ammonia solution will end up as a waste amine, a leftover from the catalyzed reaction.
So, you've wsahed, scrubbed, washed and scrubbed, and rinsed under running water. Now let dry, rough up everything with 80 grain and wash everything again, let dry, and add the next layer or the epoxy top-coat if the fisheye layer was the top layer. let if cure well (how about a couple lights under a drop cloth to warm the air and speed curing?), then sand smooth. That should do it.
Personally, I no longer use the exorbinantly expensive epoxies with fancy pumps. Give me a simple epoxy that mixes by a simple whole-number resin to hardener mix ratio...by volume...and I'm happy.
Let me know what's up and what happened and we'll find an answer
best and have good T-day

Mike and Rikki