Best to disable the AVR chip.
Fair enough. You are absolutely correct, depending on what you use this USB/Serial interface for you may need to disable the chip. But for the majority of applications, I haven't had any issues with not disabling the on board ATMega328.
My reasoning is that the bootloader interact with the Rx/Tx line only during the first few seconds of the initial power up, so if you can avoid using the serial port during that period of time, you should be OK (according to my experience). That said, whatever the program is on your AVR should definitely not use any Serial routines.