If you have a sole proprietorship or single member LLC, then the IRS does not recognize your business income as being a separately taxable entity. It's a disregarded entity which is reported on SCH C as a physical part of your personal 1040 tax return. It flat out does not matter in any way, form or fashion if you will be filing MFS or MFJ. It's still "YOUR" business, and *ONLY* your business.
Do note that for a married couple to file separately will practically ALWAYS result in you paying more taxes.
