1. Yes and No. The payments you make should be based just what you would owe, however, when doing the calculations, you should consider how much he makes so that you are making the payments that are ordinary income taxes based on the correct tax bracket. For example, if you make $55k from your business and he makes $55K from work, and you calculate your taxes based on Married Filing Jointly, then you would both only have withholdings at the 12% bracket, when in reality it should be at the 22% bracket. So, you don't need to pay taxes on his, but you do need to consider what he makes to properly calculate your tax rate.
For your self-employment taxes, his income does not affect yours.
2. Yes. At the end of the year, when you say this is how much I actually made by filing your tax return, then the payments that would be due for SS and Medicare are made there. You do not have to do anything special to direct the money to go to the correct place.
3. To not be penalized you would need to pay 100% of your last years tax LIABIILTY for your return, not just your business. This is found on line 16 of your form 1040.
4. No. You are never penalized for overpaying, only underpaying. If you want to overpay, that is perfectly fine with the IRS.
5. Your 1040SE attaches to your form 1040. You will only send this in when you file your actual return. You can either send in your vouchers quarterly or pay online directly at IRS Direct Pay.
6. No. There is no paperwork to fill out to let them know you are making uneven payments.
7. Yes, if you overpay, you do have the option to get it refunded or you can have it applied to the next years taxes.
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