Where do I enter my 1099-MISC if it was a bonus from employer and not self employed income?

It would still be entered into return and treated like self-employed income because you would need to pay FICA taxes from this income.  In your return, it will be called a self-employment tax but in reality, it is a FICA tax that needs to be paid on the bonus.

Thank you, there's a few odd questions I have to answer that don't really apply since it's not self employed money.

Yes, I do realize this.  You just need to answer those questions to the best of your ability.