Custom PCB board Based on atmega32u4

I created two versions of PCB. One included ICSP and 2nd without it.
In the First board, I uploaded a bootloader just like Arduino Leonardo using ICSP pins and then upload the actual program using the USB port and it works fine.
Now I want to upload the hex file generated by Arduino IDE in the temp folder to the 2nd PCB without any bootloader with a programmer tool i.e Xeltek SuperPro 610 and a QFN Socket. I used 16 MHz crystal on PCB and power will be through the USB port. I also want to lock the code so no one can read it except erase it. I never set up fuse bits before so I guess, I am doing wrong at this stage because the program is not working at all. It would be very helpful if someone can guide me about it. Any suggestions or hints are highly appreciated.
Also, Am I uploading the correct file generated at the temp folder after compilation i.e. blink.hex(not with bootloader one)
Thank you