We were in exactly the same situation (except it wasn't the schools account it was the City's EIN number - don't ask
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Before you can apply for 501c3, you need to line your ducks in order first. You need to get your own EIN to get your own bank account. You need to create a Charter or by-laws if you don't already have them (the IRS calls this Articles of Incorporation).
The form is daunting but it is not as hard to fill out as it looks at first. It will take some time. The application fee is $500 for the IRS. We had a CPA volunteer to help us but he mainly helped to organize the responses we provided.
After you get approval from the IRS, there is probably a separate process to get recognition from the state (in MA it is called being a Public Charity and that allows us to avoid state sales tax).
We were encouraging the other PTOs in town to do the 501c3 thing too, so we put together a slide show of what needs to be done. It is posted at this URL
www.macarthurschool.com/pto.htm
and click on the "Guide to getting Non-Profit/Tax Exempt for a PTO" link on the right hand side underthe link to the PTO's Charter.
Good luck.