I followed the steps described in section 3.7.2 of attached manual. There is no need to open Control Center and upload the firmware manually. May I know which maual do you refer to that needs uploading the firmware by USB Control Center?
C.1 of Getting Started with EZ-USB FX3 mentions: "The Segger J-Link probe is the preferred JTAG probe for the FX3 SDK".
Since the SuperSpeed Explorer Kit has an build in OpenOCD, your manual only shows how to use the OpenOCD, unfortunately the J-Link way is different, since the arguments will be different. To figure out these arguments (for J-Link Commander) is exactly the problem that I have.
The USB Control Center is mentioned in section 4.4.3 of FX3 Programmers Manual and is currently the only way I found to upload firmware without debugging the device. Also the only way I found to program the flash.
So having two different run configurations one for a control center style upload - requiring the bootloader mode - but beeing able to upload to ram and flash, and one configuration for JTAG (J-Link) to just upload in ram (and don't care about the mode), would be a master class solution. For now I would be happy with any one of these.