A few years back, I was in your shoes. I was treasurer for one PTO that had a personal SS# on its bank account, and then a year later, for another PTO that used the school's EIN number. Yikes! I learned that in both cases, it was best for us to create "new" organizations by incorporating in our state (never had been done before) with their own EIN numbers. The IRS views incorporation as the begin date of the organization, so when we filled out the 501c3 application (Form 1023), we did so as though the group was brand new, even though we had a balance in our bank account (no problem with the IRS on that).
One really imporatant decision you need to make is whether your PTO is acutally an independent group from the school or a committee of the school. If you want to be independent, you need your own EIN, bylaws, bank account, annual IRS forms. But if you are a committee of the school, your banking will be done through the school's account, and so you dont' have your own EIN. In that case, your money is really owned by the school but they let you manage it as a courtesy.
Assuming your PTO wants to be an independent group, you should follow JHB's advice and start new, even if you don't incorporate (incorporation typically gives the officers protection from liability, but you can also buy insurance for that if you decide to skip incorporating for some reason). Don't worry about what's happened in the past. The IRS has better things to do than chase down delinquent parent groups (though of course it's within their right to do so....!). Now that you know, do the right thing for your group. Be sure to follow through, and---very important--document the ongoing responsibilities for the future treasurers (ex: annual IRS Form 990/EZ) so the next treasurer knows what to do. Once your PTO becomes a federally-registered 501c3, you need to continue to act like one forever.
Yes, I would recommend the start-up tool kit. It explains all this organizaitonal mumbo jumbo in plain language. Plus is takes you thru the 501c3 applicaiton item by item, step by step, in PTO language. Also, don't be afraid to call the IRS with your questions. The reps can be very helpful.