When you said you "finally got the tank established" I assumed it was cycled. Established
is the term usually used to describe a cycled and mature tank. Your ammonia problems indicate that it is not, or at least it is not a strong enough cycle. Dose Prime @ 2-drops daily until your ammonia and nitrite read 0.0ppm.
Here's the reference you want: CYCLING: the two-sentence tutorial
As Mike suggest, smaller pellets or ground up ones are better for your water quality than flakes. Besides they're more nutritious.