You need to find out what the status of your organization is. An EIN (Employer Identification Number) is just a tax identification number that any entity can easily get. (One page form, fill out online, over the phone, etc.) It doesn't have anything to do with your status.
Ideally a PTO has the status of a tax-exempt charitable organization. You get that either by filing the appropriate application with the IRS to becoming a 501(c)(3) or following all the same rules but having less than $5000 gross income per year. (Thus, being so small the IRS doesn't really worry about you.)
The problem is that many PTO's never formalize even though they exceed the $5000 rule of thumb. Thus they aren't really operating legally.
I'd contact the IRS with your EIN and see how they have you listed and how they want you to submit organization changes. Once you know your status you can decide how to proceed.
I haven't a clue if they have filed. I was reading on IRS website about filing 990n (ePostcard) and it said to file every year by the 15th day of the 5th month after you close out your tax year. So if we close out in May, we have until Oct 15th to file...