@Dblunt99 

If you work there, you are an employee and get payroll and a W2. This would be more like a commission from a specific job you brought to the business, and of course anything they pay you goes through your payroll.

That means it is business income as usual, and the payout is your wage (their expense) as usual. Even if you call it bonus and not salary or hourly, it's still wage compensation.

You never want your employer to keep your money.

I don't know how you ran your side business through theirs. That is never a good idea. You are blurring the lines for customer, provider, risk (insurance) liability, supplies and equipment. It's either your business or it's theirs.