wow james!!! are you THE james tichenor?
nice to see you here!
i think the problem is that even if you select DAPA as a programmer you still need to pass it the name for the right parallel port while the arduino ide will let you select between serial ports....
in general when you use arduino to compile some code there will be an .hex file in thedirectory where the .pde file is
you can use and windows tool that came with AVRISP to upload this hex file to the board
what do you think? not smooth enough?