OK, I'm trying to use the USB > serial on the UNO, via the /dev/ttyACM0. I already know that you can't have 2 programs compete as the first one open will get dibs. You close the IDE first then try Minicom or other program. Despite being in the dialout group on my Ubuntu 13.04 box I still have to use sudo in order to READ serial output with Minicom. I have one UNO I'm trying to make into a timer and it counts seconds readable on Minicom as described above.
Now, I deployed a second UNO that'll take in a number from 0 to 15 to toggle relays and output the binary and decimal of the number typed - but only through the IDE's own serial debug feature. If I try that UNO with any other terminal program I can type in a number and the cursor keeps blinking in the same upper left corner and relays don't toggle according to the sent nybble in decimal.
Of course, if I plug in both, the first one (the one with the relays) is the /dev/ttyACM0 and the second one is a /dev/ttyACM1. With both, I can select between the two with the IDE to align a sketch or use the serial feature.
In the Arduino Playground section of this site has a command line article with this loooong command (a ton of "switches") to set the port. I tried it and poof the UNO with the relays resets (of course) but won't take nybble commands over the serial. I'd like to write shell scripts to control relays to do lights like Clark Griswold. But, like the Minicom problem, it's a no dice.