Mega Pro 3.3V and ftdi cable?

Hi

I have done a labproject where I have used the Arduino Mega but now I want to go for 3.3V and then I will use your Mega Pro 3.3V. I want to build into the Pro 3.3V into a box but would like to be able to program it from outside the box. I would then prefer a cable that is robust and then not use any breakout board. Is that possible? I have seen some posts about RTS/DTR differences which I don’t understand completely. WHat connector do you think i shall use on the box to make as little confusion as possible?

/Patrik