There is no difference. You might want to setup a second schedule C if your self employment business is different than the contractor income. The 1099Misc contractor income was also self employment income.
It's the same field. I was working at a salon, now I have a home salon. I'm not sure if the program will let me shift gears from having an 'employer' for part of the year to being 100% self employed, and I certainly want to get all my deductions!
Just continue on in the same schedule C, the same way. When you were a 1099 contractor you did not have an employer (if you were an employee you would get a W2). You were self employed for the 1099 contractor income. You report your self employment income the same way, wether you get a 1099 or not.
At the salon the "employer" was really your client just like your clients now. You just don't get 1099Misc from the individual people who pay you. Enter the cash on the same schedule C as Cash or General income.
Here is some IRS reading material……
IRS information on Self Employment
http://www.irs.gov/Businesses/Small-Businesses-&-Self-Employed/Self-Employed-Individuals-Tax-Center
Pulication 334, Tax Guide for Small Business
http://www.irs.gov/pub/irs-pdf/p334.pdf
Publication 535 Business Expenses
http://www.irs.gov/pub/irs-pdf/p535.pdf