Ardunio Duemilanove ATMEGA & FTDI issue

Let me preface this with two comments, one the Arduino is a great tool and from what I have learned so far a very versatile one and two I am just beginning to get into electronics but have 30+ years in IT as a System Engineer working with med to large Windows Networks and VMware.

I am currently working on an attempt to combine two Arduino based projects. The first being a connection between an Atari 800 computer from the 80's and a PC to allow the PC to serve as a virtual floppy drive via software as outlined here http://forum.arduino.cc/index.php?topic=19177.0. I have been able to get this working but the process required the removal of the ATMEGA from the Arduino as it was interfering with the TX/RX coming thru the connection to the PC, more on that in a moment.

The second part of this project is to incorporate the unit here http://www.whizzosoftware.com/sio2arduino/index.html utilizing the same Arduino board as that first project but it requires the ATMEGA to be in place for the programming and operation. It uses the same pins for TX/RX but I need to make sure when the unit is used in one mode (direct to the PC, link in first paragraph) the ATMEGA ignores the TX/RX as it appears to not pass the data to/from the USB port but when in the other mode the ATMEGA is used so the programming and SD Card work correctly. I am thinking that to accomplish this would require some programming and teach the ATMEGA to use the TX/RX in both modes instead of the FTDI being used in the first and the ATMEGA in the second.

I am not an electronics person, nor programmer, but read a schematic and dig thru documented code to try and figure it out. If I can find a way for this to work with a single Arduino that is my ultimate goal. Any assistance would be greatly appreciated.

T.E

I what way is the Atmega interfering with the Rx/Tx signals in the first case?

I haven't tried this but I wonder if you wrote a short program for the Atmega that just loops around doing nothing would it just ignore what's on the Rx/Tx pins?

...R

When the ATMEGA is connected it appears that it is either stripping the information be sent over the TX/RX on its way to the USB port or as there is no code in the ATMEGA to tell it where to send the TX/RX data it is never reaching the USB port. Thinking about it I believe the later is the case and the ATMEGA only contains the default bootloader and the Case 1 application does not require and code on the Arduino where as Case 2 does require code. I think the solution is to code the ATMEGA to transport the TX/RX data to/from the USB as the FTDI does without code. The other solution would be to programatically turn off the the ATMEGA recognition of the TX/RX when Case 1 is in use and turn it back on when Case 2 is in use.

Thoughts?

T.E

Is anyone able to provide any insight into this issue?