Look at the Arduino schematic and get the pins for the 6-pin ISP header, and also for the FTDI header. If the 6-pin header has all the pins that the FTDI header does, you can wire up an adapter.
You can use a ladyada usbtinyisp to put whatever you want on it since it has the 6-pin ISP header. I believe you can load an arduino bootloader on it, or you can also just put C on it. Just using avrdude to flash C to it is like .0001 harder than using arduino; it's not a big deal.