If he doesn't amend his return and pay back the ill gotten gains in about 18 months to 2 years you BOTH will get a letter telling you both that ONE of you filed incorrectly and needs to amend their return.   If neither person does then in another 3 to 6 months you will both get another letter requiring you BOTH to prove you have the right to claim the child.   The winner gets to keep the money ... the loser gets to pay back the money with penalties and interest added on  AND  the ability to claim the EIC taken away for up to 10 years. 

So I already proved my right to claim our son with court paperwork (I was able to amend because of a little clause in our custody case stating that if he fails to pay all child support, then I get to claim him), will I have to prove it again? I'd just send the same paperwork.. Also, he moves around every couple of months so any mail he receives from court never reaches him, I suspect the same will happen with mail from the IRS and he will never respond.  

@amberduhh The IRS cares who is the custodial parent---the parent the child lives with the most--at least 183 nights in the tax year.  As far as the IRS is concerned, that is who can claim the child.  If you and the other parent have a signed Form 8332, then the non-custodial parent can claim the child tax credit, but the custodial parent retains the right to file as Head of Household, get earned income credit and the childcare credit.  If there is no signed 8332, then the custodial parent can get child tax credit too--which must be what you referred to when you said you got $2000.

Whether your ex gets the mail and responds to it is in the category of not your problem.  If and when YOU get any mail from the IRS, respond appropriately and promptly to provide whatever information they request.

If anything--be prepared to prove your child lives with you.  School and medical dental /records can help with that.

To clarify what xmasbaby0 said, the IRS doesn't care about that "little clause" in your custody agreement, and the IRS is not bound by the custody agreement. Showing them what your custody agreement says doesn't do any good, because it has no effect on who the IRS allows to claim your son. All that matters to the IRS is what the tax law says. (They probably accepted your amended return at face value, without really investigating.) xmasbaby0 told you what the IRS does care about, which is who is the custodial parent according to the tax law, and whether the custodial parent gave the noncustodial parent a signed Form 8332.

To try to head off trouble with the IRS, you might want to talk to your lawyer and see if there is anything you can do to get the father to amend his tax return now, instead of waiting until you get that second IRS letter and have to prove that you are the custodial parent according to the tax law.