WiFi shield, uploading firmware to blank chip.

I have been designing a board with Wi-Fi shield components (from the original eagle files) (32uc3, HDG204, flash chips etc) and a 328p for powering off a battery, the Wi-Fi subsystem can be switched off when not in use for power saving.

My question is, can I just put the USB connector on the board and upload code to the 32uc3 as described in the firmware upgrade tutorial?; or is a bootloader involved beneath the hood which I will have to program the chip with first?; before I can flash the firmware for the Wi-Fi functionality.