I am currently in a middle of a divorce, it was ordered I get the house, which I currently reside. The soon to be ex-wife had to move back in due to no job, getting kicked out of her apartment, and had also just recently been kicked out of her friends place. Seeing as we have a child together and she has no place to go unless it was her parents whom live 5 hours away (which means very limited time with my son), I agreed to let her move in until she finds a job. Does this adversely effect my divorce agreement as we are not officially divorced yet? Also since she has nowhere to live, but has primary custody (joint)of my son how can I get sole custody of him to ensure his safety, and needs are met as she obviously can not provide for him? Please note this is in Arizona which is a mother sided state. She has also tried to get me to go out with her and her mom to talk about things, but refuses to do it when it is just the two of us, last time that happened all they did was try to threaten me and claim they will take it all from me. She also uses the excuse she has no money, and feels awkward living in my home although we seem to get a long though it's for my son's sake, and she seems to be fine until I try to help her find jobs or suggest ways of getting one.

There is no divorce police. But exes beware, when one ex flies off the handle and uses whatever they can as ammunition. You just don't know, and you don't know what her lawyer might decide is good fuel for the fire.
Of course you are being good hearted, she is out of work, and you care about your son. All that is admirable.
I would talk to your lawyer if you can afford it, or take someone as YOUR sidekick when you have a sit down with her and her mother. Better yet, find a mediator who is cheaper than a lawyer, and insist on going alone with her. Watch out for recorded conversations too, on cell phones even.