You will need to activate self billing on a per-employee basis. By default, if you have the self billing module, then when you create a new employee, he or she will be enabled by default.
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To enable or disable self billing for a specific employee, you need to edit their employee record. Click on System Management in the left-hand menu, then Employees. Find the employee you're looking for and click the pencil / edit icon at the end of their row. Click to the sixth tab along, Self Billing Details, and, under the Self Billing details tab at the top, tick Enable self billing for this employee. Then click Update at the bottom of the page.
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Don't forget you will need to enter the employment details for the employee, e.g. Limited Company name and registration details, or details of their self-employment.