I haven't worked with that specific board, but it is in the pulldown menu of Loader, so that's good news.
Do you have the "serial programmer cable" mentioned in the directions?
Right now the only firmware that is compiled for that board is the "LED blink test", so you'll need to compile a hex file from the source code (or get Jon to do it ) so you can use "File -- Load HEX File" menu.
Which firmware were you wanting to use? (HID joystick, MAME P1 defaults, etc.)
Scott