Support for the FTDI chip on the Arduino board (232BM) is, according to the FTDI website, built into Linux kernels version 2.4.20 and later. If the PMA400 uses a recent Linux kernel, it should be able to communicate with the Arduino board. The Arduino board should show up as a serial device (e.g. /dev/ttyUSB0).
Getting the Arduino software running under Linux can be a bit tricky; you're probably better off programming the board with a Mac or PC. If you'd really rather get the IDE running on Linux, see this forum thread for help: