Your post brings up a lot more questions. How is the business set up? Is it a LLC or Partnership etc? Do you file a separate Business return? Like a 1120, 1120S or 1065?
Will you be getting a W2 or a 1099Misc for your pay? If you are an owner you don't usually report payments to yourself. If you and he report it as self employment you are not an employee of the company.
And usually if you are married it is better to file Joint instead of separate. Joint has the lowest tax rates and the highest Standard Deduction. And you can lose several credits by filing separately. like the
EITC Earned Income Tax Credit
Child Care Credit
Educational Deductions and Credits
