1. Yes, @Carl is correct that you could pay in a rough estimate by using gross income. The estimates are paid at 4/15, 6/15, 9/15, and 1/15. Otherwise, yes, you would use your profit and loss year-to-date to calculate the net income. This would capture the income and deductions and be closer to the actual self-employment tax.
Another way to know the amount of estimated payments to make would be to use QuickBooks Self-Employed, which calculates these amounts for you. This article explains where to go to login and what to do. How do I access QuickBooks Self-Employed?
2. Since your wife is getting paid by a W-2, it could affect what tax bracket you have for the income tax portion of your income.
3. Yes, by paying estimates in quarterly, there will not be as large of a tax balance due at year end. These can be paid by one of the following methods:
