Thanks for the reply.
So power the board with the 3.3v FTDI and at the same time send 5v to the raw pin to supply the sensor?
I was hoping to wire the 5v sensor (DS1307 RTC) like this:
The voltage regulator would be 5v (with 0.1uf capacitors in and out) and the Arduino board is the same one as the link you provided.
So how would I make sure the I2c lines are pulled up to 3.3v and not 5v? do I remove the 4.7K resistors from the RTC and place them somewhere else?](Photo Storage)