Both will still work, much the same as if you have a Zorro graphics card in a standard box box Amiga like the A4000. All standard Amiga display output generated by the AGA chipset will still be sent to the standard Amiga graphics port. To see anything from the graphics card you need to be using the specific graphics devices that are for the graphics card. Then the display will be seen on the graphics card instead of the standard Amiga output.

This is why some people use a TV card in their Amiga tower conversions, so they can pass the output from the standard Amiga monitor port into the TV card so it can be seen on the graphics card display. Not sure how well this works though.