Yes, the amount found in Box 2 of 1099-MISC are for the royalties fees that are paid to the franchiser.
As a franchise operator the amount is reported on your schedule C as a business expense.
The following TurboTax products can be used for reporting self-employed business.
Generally, it is not necessary to issue a 1099-Misc to corporations, with a few exceptions.
The following types of payments require a 1099-Misc to be issued to a corporation;
* Medical and health care payments reported in Box 6
* Gross proceeds paid to an attorney in Box 10
* Payments in lieu of dividends or tax exempt interest in Box 8
I am including the instructions for the 1099-Misc if you need more detailed information: