The X5000 only has one PCIex16 slot so 2 pciex16 cards cant be installed at the same time unless you can get an adapter to work. Either a pci to pciex16 adapter or a pciex1 to pciex16 adapter. If the OS does not support the graphic card in the primary slot (The PCIex16 slot) then you will not get a display. Also It appears that currently both MorphOS and AmigaOS 4.1 do not support multiple Radeon cards on the X5000.
So to run MorphOS on the X5000 at present you will have to remove your Radeon HD Southern Island card.