If you aren't putting a 100nF capacitor between the FTDI's DTR and the ATmega328's RESET pin, you don't have auto reset. You'll need to reset manually (and leave DTR disconnected).
If you aren't putting a 100nF capacitor between the FTDI's DTR and the ATmega328's RESET pin, you don't have auto reset. You'll need to reset manually (and leave DTR disconnected).