I installed the usa firmware using the flash way, but I notice some people flash the emmc vanilla file bin first then the firmware , what is this emmc vanilla bin for anyways?

Flashing the emmc overides the contents of your MyDocs folder, which means you could potentially lose lots of user created stuff and settings, even if you do a backup and restore. In general, there is very little need to flash the emmc. Perhaps if you were wanting to totally wipe the phone prior to sale or something like that...