Re: I own the LLC and want to file taxes married filing jointly quarterly, I have a W2, Spouse has 1099
You will need to combine both your income and expenses together with her income and expenses in the same company file.
Note that this will result in ONE Schedule C on your tax return. Since the 1099's are in her name, this will be her business on the Sch C. If you also receive 1099 income, you will need a new plan, as IRS will expect to see another Sch C in your name. When the big computer can't match your 1099 to a Sch C, you will get a letter. If you both receive 1099's, then you will both need a Sch C.
If you want two Sch C's on your tax return, then you need to create two QB companies and track everything separately.
If you want to combine everything into a single QB company to save a few bucks, you will need to split everything out manually at tax time. This pretty much negates any advantage of using QB. So compare the cost savings to the hassle cost.
Your W-2 income is outside the QB company.
Mark Wagner, CPA