Maynard,
Sorry, we at the CCS forum are not the most knowledgeable about the different flashing mechanisms of AM335x devices. There is a tool called Uniflash that supports Sitara processors, but the information on the page below does not mention eMMC:
http://processors.wiki.ti.com/index.php/Sitara_Uniflash_Quick_Start_Guide
From inside CCS, the only way I see this being possible is if an example project performs this task - I am unaware of such thing. The CCS/JTAG does not perform external flash programming of any kind, as the number of flash IC vendors and the possible combinations of interfaces (SPI, parallel, I2C, etc.) and the physical arrangement varies greatly from board to board.
Regards,
Rafael