The SX2 configuration registers (EPxCFG) that configures the endpoint buffers are initially set to match the default descriptor endpoint configurations, which are also the default values shown in the datasheet. These registers control the direction and length of the endpoint buffers. Please look at the datasheet for the boot methods. If an EEPROM is attached with only a VID/PID/DID (6-byte sequence) or if the external master writes only the VID/PID/DID, then the SX2 enumerates with the default descriptors and the endpoint buffers are configured accordingly by the default values present in the SX2 configuration registers.
Otherwise if the entire descriptors are loaded from EEPROM or the external master writes the entire descriptors, the endpoints must be configured through the command interface according to the descriptors.