I don't think there is an answer to how you report this every year (the way you want to) since it sounds as if the earnings shouldn't be handled this way.
The issue I see is that the amount received is for work you performed as a W-2 employee, in which case your employer should have reported in on your W-2.
Why does this matter?
As an employee, both you and your employer contribute to your FICA tax (Social Security account). The pay and the tax paid is listed on a W-2.
In your case you want the pay listed on a 1099, and it sounds like you are willing to pay the tax (federal income tax and/or FICA ? ) but if you don't file Schedule C, the federal tax could be reported, but the FICA won't be computed correctly. The half the employer pays won't be paid. The half calculated from the self-employment income won't be computed.
The IRS allows for situations where a Taxpayer may get a 1099 and pay income tax on that amount, but not for a situation that occurs year after year. The exceptions pertain to things like prizes, fellowships, and stipends. Not pay earned for working as an employee.
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