1. No, you can still use a Discrete GPU instead of the iGPU if you want more performance but it will run at PCIe 2.0 x4.
2. I am unfamiliar with ASRock boards but you should have an option in the BIOS that says 'Advanced Chipset Configuration" and you should be able to select the Primary Display Adaptor to either Onboard or PCIe, if you cannot then you may need the newest BIOS for the motherboard (Link)
3. You can use Dual Monitors with the Athlon or a Discrete GPU from my understanding.
Hope that helps
Check page 47 of the motherboard manual. It explains what sgtbilko is talking about. Choose PCIe and shutdown. Then move the monitor cable to the vidcard output before you restart.
Just to note, you are not currently able to run the drivers for the APU's integrated GPU at the same time as the ones for your Nvidia card.
If you would like to use the APU's integrated GPU you would need to connect the monitors to the Motherboard and install the AMD drivers. You should be able to find the AMD drivers for your system at: www.amd.com/drivers
If you would like to use only the Nvidia card on this system you would first need to make some changes to the BIOS. Enter the BIOS of the Motherboard and click on "Advanced > Chipset Configuration". Once there change "Primary Graphics Adapter" to PCI Express.
Once you have done that click "Exit > Save Changes and Exit", at this time the computer will restart and will begin streaming the video to the Nvidia graphics card. As such you will need to make sure that the monitors are connected to that card.
Once the system starts you should then be able to install the Nvidia drivers. If you have installed any AMD display drivers on the system you might need to uninstall these prior to installing the Nvidia ones.