Connection to PC via 2560's serial0 does not depend on bootloader (if you plan connection when main program is running). You need 16u2 running to bridge 5V serial UART to USB or you can of course use any other option (e.g. MAX232 or so) to convert 5V UART to USB or RS232. But in case of RS232 double check baud rate error because of 16MHz crystal for particular baudrate.
2560 bootloader just implements firmware flash.