I am employed by a nonprofit that has its own EIN. My payroll funds are covered by the nonprofit. However, my organization pays a local for-profit company that is not a payroll processing company to do its payroll. The for profit company is a completely separate and non-affiliated organization that has a tie to the nonprofit as the CEO of the for-profit is the founder of the nonprofit, so he allowed us to "hire" the for-profit to do our payroll. I just found out that my payroll records are being reported under the EIN of the for-profit company (the non-profit is mentioned as a cost center to the for-profit company on my payroll stubs). They are not using the nonprofit's EIN when processing payroll. So, when I file my W2 it will state that I was paid by the for-profit and not the nonprofit. What are the IRS requirements for reporting payroll under your own EIN? What are the risks to the organizations and to me if my payroll is reported under the EIN of the for-profit and not the non-profit?
Who employs you (as identified by the EIN on your W-2) is irrelevant. Regardless of what entity pays you, and regardless of the tax treatment of that entity by the IRS/State, your income is earned income and is therefore taxable.
"What are the IRS requirements for reporting payroll under your own EIN? "
The statement "your own EIN" indicates that you own the business. If the business is a sole proprietorship or single member LLC then under no circumstances can you the owner be an employee of that business. That's because the IRS considers a sole proprietorship or single member LLC to be a disregarded entity. The owner of a disregarded entity can not also be an employee of that same company since the earnings/losses of said business are reported on SCH C as a physical part of your personal 1040 tax return.
If your business is some other type of entity such as an S-Corp, and your business pays another business (of any type) to "deal with" anything pertaining to your busiiness, then what your business pays that other business for the products and/or services they provide is a bonafide business expense. But it is not a payroll expense if your business does NOT issue paychecks to a living, breathing individual.