I sugest you get hold of a few spacers and create holes in the plate that holds the PC motherboard to mach up with the existing holes in the A1200 motherboard.
You could also either just use extension cables to the Amiga ports though this is much work or you could cut out at the back of the tower and let the ports stick out.. also a bit of work though in return you could use the ends of the cutout to make holes and use the screws for the port to fixate the card to the back for better fixation of the motherboard.
