I recently created a pcb with the atmega32u4 to use it as a development board. The controller is connected to a micro usb port. Should I install the arduino bootloader instead of the deafult one? Or keep the default boot loader and find another way of flashing hex files? But bottom line what is the process to flash a hex file to the atmega32u4 via usb?
Installing the Arduino bootloader would make it easier to upload you sketch from the Arduino IDE.
Installing the Arduino bootloader via DFU is probably the easiest method. Alternatively use ISP, but you'd need a programmer for that, or use a separate Arduino board with the ArduinoAsISP sketch running on it.