sdinnu:
yea that makes sense, so either inside my project or outside my project there would have to be some usb->ftdi->ttl converter to be able to do the serial communication that the arduino IDE requires correct?
It depends how you are planning to reprogram. If you are going to distribute a "box with firmware upgrade" on it, that would be TTL to TTL, so you wouldn't require that. If you are going to use the existing bootloader and use, say, a laptop, then you would need a FTDI cable, and some adapter to convert it to the mini-USB plug you are planning on.