FTDI USB Chip in UART Mode and Bitbanging at same time
The Bit bag modes only apply if NOT using the UART. All 8 lines are switched at the same time when changing the mode. You could use one if the 2 in bit bang and the other as UART. 
http://www.ftdichip.com/Support/Documents/AppNotes/AN232B-01_BitBang.pdf