If you are an independent contractor, then you have a business accounting file. The 1099 is info, it is telling you that you were paid that amount by someone and it is reported to the IRS too. The only impact that has on your tax form, is the when you enter total sales, it has to be entered in two blocks, amount reported on 1099's and income made but not on a 1099
filing jointing, both your incomes are combined. Fill out your business tax form, if it is a schedule C, then it is included with the form 1040, it is a partnership, then the partnership filed a form 1065 and gave you a form K-1 for your share, that K-1 is entered as part of the 1040 too.
Estimated taxes are a personal responsibility to calculate and pay quarterly, correct QB does not make the payment.
State taxes I can not help with, my state does not have personal income tax. But it sounds like you should talk to a local tax accountant.