I'm designing a board that needs to be programmable via USB and external TX/RX pins. I decided to use FT232RL ( http://www.sparkfun.com/datasheets/DevTools/Arduino/FTDI%20Basic-v21-5V.pdf ) for the USB interfacing. For the external RX-TX pins, do I need any logic or jumpers to disable the FTDI chip, or simply if there's no D-,D+ signals, I can use external RX and TX pins, that are connected to both MCU and FTDI, without FTDI chip interfering. Any help is greately appreciated.
For TTL serial (and other logic devices in general) connecting one output to two inputs is typically OK, but connecting two outputs together is a no-no. In this case with the USB side disconnected the TXO line will be driven high which is the normal idle state for TTL serial. Then the programming port won't be able to reliably drive the line low and even if it can it might cause excessive heat dissipation and component damage.
So you'll want a jumper to switch between TXO on the FTDI module and TX on your programming port so that only one is connected to the RX line on the microcontroller without them being connected together. For the TX output from the microcontroller it shouldn't matter if it's connected to both, as long as you're OK with data being sent to both while programming. It won't cause a problem with the FTDI module but does mean "junk" will be sent out over the USB CDC port if it's connected and open during programming.