Self employed

What does the other spouse have?  Income from self-employment?  W2 income?  No income?

does it matter if the person paying the tax is the one without any 1099s? If you are married filing jointly, basically, your liabilities are coming out of the same pot on your tax return, so there is no difference in who pays the actual tax.  

Now for Social Security, if both of you are self-employed in different businesses, you should have 2 Schedule C's.  You would enter your income on your Schedule C and her income on her Schedule C.  This will report your individual income to your individual SSA accounts.

To get TurboTax to do two separate schedule C's you will enter the income and expenses for the first person, then when done, you will select Add a Business and enter the income and expenses for the second person. 

 (HOWEVER, if you are partners in a business, then you would need to file a partnership return 1065 instead of a Schedule C and then enter your individual K-1's, unless you are in a community property state) 

If she is the only one that is self-employed, then she is the only one that should have a Schedule C.  Your name would not be on it. 

Basically, your incomes are separately reported, but your payments on a joint return are all coming out of the same numbers.  One persons payments will offset the other persons liabilities and vice versa.