Ok let's take your questions one at a time:
I will start with the gen calculator,
the first column is the Locus which is the name of the gene on a specific spot in the genetic code(put simply), ex: the gene or Anery or Amel or Motley.
The second column is where you select the genetic make up of the dad.
The third column is where you select the genetic make up of the mom.
Below the column is a click button that says percentage and if you click it, once you have entered the genetic info and clicked calculate, it will show you the potential off spring on the right of the columns and it will show you the percentage break downs.
Now your Anery was from a pet store so the only thing you know for sure about it is the fact that it is homo for Anery(it shows Anery or simpler put you need Anery to make it look that way). I am unsure if you know it's sex but for the example we are going to say it is the dad. Now you would go to the Locus column for Anery and under drop down under the male column select Anery.
Let's say you bought another Anery female(just to keep things really simple) and it was from a breeder and they told you she was not het for anything. You would then go to the Locus column and look for Anery and in the corresponding drop down under female you would select Anery.
Now you have selected all of the genes at play(that you are aware of) remember your pet shop purchase may or may not have surprise genes. So now click the calculate button and you will see that you are going to get:
100% Anery
This is because the only gene represented in both parents was Anery.
Now this is just a computer program it can not account for unknowns, such as the possibility that your pet store purchase might have hidden genes.
So let's take another ex. and say that your Anery is actually Anery het Amel (amel is a very common gene) and you bought a Snow hoping to prove whether or not your Anery had Amel as a hidden gene.
I was looking at the anerythristcs on that website and they were all an^a an^a. The amelanistics were all a^a a^a. The snows are shown as a^a a^a an^a an^a Are they all homozygous or just the ones they were showing or do I just understand how they are posting their genetic makeups?
The genetic make up of a Snow is full or homo Amel and full or homo Anery, meaning both parents had to carry both genes in either the homo or het form to be able to make a Snow. If one parent had both genes and one parent only had one gene you would not get the Snow that is why they show the gene code for both Anery and Amel genes being present under Snow(hopefully that makes sense).
So the pairing of your Anery(if we are saying it carries Amel) to a Snow would be entered into the calculator like this.
Still going with your Anery as the male.
Under the Locus column find Anery and the corresponding drop down under male and select Anery, then under the Locus column find Amel and the corresponding drop down under male and select het Amel.
Going with the Snow as the female, you would look under Locus to find Anery and and the corresponding drop down under female and select Anery, then under the Locus column find Amel and the corresponding drop down under female and select Amel.
Click percentage button and click calculate and it will tell you:
50.0% Anery het Amel
50.0% Snow ( Amel, Anery )
So if you bred your Anery to a Snow and the above were the results then you would know for sure that your Anery was actually Anery het Amel. You would then have proved your Anery to be carrying the Amel gene.
If you did that pairing and got still got 100% Aneries then you know that your Anery is not carrying the Amel gene but it still may be carrying other genes. As well because you had done the breeding of Anery to Snow at the very least you would have 100% Anery 50% ph Amel which means that because one parent had the Amel gene then 50% of the babies will carry it and 50% will not(but I still have no idea how you would tell).
But apparently anerythritics are just boring to breed as far as varied offspring is concerned. Amelanistic and snows are still worth a shot since I'd be getting normals with anything else I may breed her with.
So hopefully you can see that trying to breed for a desired result when you have no idea what a snake is carrying gene wise not as simple as "I like how these snakes look can I breed them and get these?" There is a lot of genetic background information that has to be understood and known first. Then if you do not know the background genetics you need to prove them out as I showed in one of the examples above.
Finally I can not help you with the Punnet Squares I have never done one yet as I am still learning the genetics and having to do a lot of reading, research, asking questions, confirming what i think I understand, getting help from my husband and members here and esp. Susan's genetic tutorial on here and Charles Pritzel's book "Genetics For Herpers".
*p.s. playing with the two genetic calculators helps me out to understand as well, that and learning what genes are needed for each morph. Here is a link to another genetic calculator.
http://geneticcalculator.traxxtec.de/en/rechner.aspx