So just because the 1099 is from Mississippi, it doesn't mean it is Mississippi source income?
That is correct - "the 1099 is from Mississippi" - means that payer is located in Mississippi and that doesn't determine the source of income.
If you were an employee - W2 form would show in which states you worked, but as a self-employed - that is your responsibility to keep track of places where the work was performed.
See for instance - http://www.mstc.state.ms.us/info/faqs/IndividualIncomeFAQs.html
How should my income be reported to Mississippi if I am a resident of another state but I work in Mississippi and other states?You must include all income on your Mississippi non-resident return. If you perform services partly in and partly out of the state, only the wages you are paid for the services performed in Mississippi are subject to Mississippi income tax. The W-2 forms issued to you from your employer(s) should indicate the state in which the wages were paid, along with the wages you earned in that state.
see also instructions page 6 - http://www.mstc.state.ms.us/nactp/indiv/2009/indiv_80100097.pdf
Enter your profit or loss if you owned a business or practiced a profession. If you had more than one business, or if you and your spouse had separate businesses, complete a Schedule C for each business. If the Mississippi net profit or loss amount varies from the Federal Schedule C net profit or loss, then provide a reconciliation. If you enter the federal amount on this line, but there is a difference between Mississippi and federal amounts, enter the adjustment on Schedule N. The federal Schedule C must be attached to your return.
Let me know if you need any help.