Generally when you install a Discrete GPU card on a Motherboard with a APU, the Internal Graphics is automatically disabled and the Discrete GPU card is made the "Main Display Adapter" for your PC.
In BIOS there is usually Settings for making your APU Graphics the Main Display Adapter or your Discrete GPU card as the Main Display Adapter. But if it is set at something like "Auto" it will make your Discrete GPU card the Main display Adapter automatically rather than your Internal Graphics.
Also could be a conflict between the AMD and Nvidia drivers.
Maybe if your temporarily remove the Nvidia GPU Card and then try to install the AMD driver it should work since your APU Graphics will now be the Main Display Adapter. Then once the AMD driver is installed and working, Reinstall the Nvidia GPU card and see if both are now showing in Device Manager or a error occurs on the AMD Graphics driver.
Your Nvidia GPU card must have more then one Video Outputs. You can always get an Active HD DP>HDMI adapter to connect your second monitor to your GPU card.
