Thanks for your reply retrolefty. To clarify based on the good questions you asked, this is what I am after.
I have no need to remove the current USB interface from the Mega. I am fine using that to update my sketch etc. I did not know there were other serial connections/options available but that sounds promising. I would like to use a FTDI connection between the pc and the arduino, potentially using this alternate connection.
The program I am running to control lights sends a DMX string over USB/Serial to the arduino. On the arduino is a sketch that basically processes the streams and makes digital ports go high/low. The current software plugin only recognizes FTDI connections, but no the new style of the MEGA. So if I can provide an alternate connection into the mega that would be ideal.
How would that be wired? Also, when I have the FTDI connected (now I have 2 serial connections right?) how do I manage the serial(read) on the arduino to choose the correct one?
Thanks!
-Rob