Chris,
Ok, so let's establish what you have...
1) Do you an AVR ISP...? Typically a little USB dongle type board that ends in a 6 or 10 pin MISO / MOSI connector? These are commonly used to flash bootloaders etc into empty Atmel ATmega MCUs like Arduinos.
2) Does the target Orange board have have the ISP MISO / MOSI programming pin set available and marked? I ask beacuse I would believe that the "DTR, Tx, Rx and GND" are a standard seial port, not an ISP port.
My suggestion is as follows. If the ISP port is definately NOT broken out on the PCB (very unusual) then I would dab some very fine mod wire onto the ATmega pins, bring them out to some vero and put an ISP header on that.
Once I had the port working to flash the chip I would maybe epoxy it onto the board for future use, else it's a lot of work and only gets used once in anger.
What if they bring out some newer firmware in future?
BTW, I have one of these Orange stabilisers, and I've looked into flashing an open source firmware onto it. In the end I built my own stabiliser and wrote my own firmware. My homebrew unit has one major design improvement...
All the cheap Orange etc stabilisers keep their price down by only using 3-axis gyros. This means they can only sense instantaineous angular movement, but once they stop pitching, rolling or yawing the output stops. They're fine for taking wind buffeting out of your flight. They don't know what LEVEL is...
My system has a 3-axis accelerometer, which knows what level is. My system keeps correcting the control sufaces until it is level. Auto-recovery.
I literally have a PANIC button, on an AUX channel that once triggered should level the plane where ever it is.
Anyway, hope that helps, I might dig my Orange unit out and see if they have broken the ISP port out.
Cheers!