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A LLC owned by husband and wife CANNOT be a disregarded entity. You cannot file as 2 solo proprietorship (joint venture election) . You have to file as partnership. Partnership is a flow through entity so eventually the tax liability will be calculated on your personal return. To make sure the payment is correctly assigned to your current year as estimate use the proper voucher and also specify it on your check as such: 2nd Qtr 2017 1040ES for instance. The same would apply to your state estimates. I would not calculate any interest or penalties, let the IRS to "figure it out" for you.
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AGI is adjusted gross income - total income reduced by certain adjustments. When you look at 1040 the adjustments are on lines 23 through 35. You can use the worksheet but most people don't use it. The easier way is to determine your tax bracket % (income tax) and add 15.3% (self-employment tax). Apply to percentage to your estimated net profit for the quarter to calculate your estimates. For instance if you are in 15% tax bracket you should estimate about 30% for federal taxes.
Does it make sense? If you are going to file a joint return it does not matter who makes the estimates. A partnership itself does not pay any taxes so the profit will be reported on your individual returns via K1.