The general rule of thumb when choosing hatching eggs for color is to hatch from the best example of that color egg you can find. For Ameraucana, you want to hatch from the bluest egg you can find, for Marans from the darkest brown egg, etc.
The blue egg gene is dominant over other egg colors, and it doesn't matter if it came from the rooster or the hen. If the hatching eggs you purchased are blue, then you know for sure that at least one parent (hen) carries the blue egg gene.
Homozygous means two copies of a gene, heterozygous means one copy of one gene and one copy of a different gene.
Here are the possibilities (I'm assuming that your hatching eggs are blue or green):
1. You have Ameraucana X Ameraucana eggs, resulting homozygous hens carry two blue egg genes, you get blue or greenish-blue eggs.
2. You have Ameraucana X ? eggs. Resulting heterozygous hens carry at least one blue egg gene. You get either green or blue eggs, depending on what they're mixed with. Birds will be EEs.
3. You have EE X EE eggs. Resulting hens are either homozygous or heterozygous, depending on what genes were passed down. Extremely good chance of getting at least one blue egg gene in the resulting hens. High probability that you get blue or green eggs, smaller possibility of getting brown or pink or other color eggs if the genetic lottery doesn't go your way and you don't get a blue egg gene passed to the offspring. If you get birds that don't have pea combs and/or muffs, that's a very good sign that they'll lay brown eggs.
4. You have EE X ? eggs. All offspring will probably be heterozygous. About a 50% chance of resulting hens carrying the blue egg gene and laying eggs that are either blue or green. Again, watch for birds that don't have pea combs and/or muffs, that's a very good sign that they'll lay brown eggs. Pea combs and muffs are very strongly linked to the blue egg gene.
