Suppose I have a good motherboard with two GPUs installed in the PCIe
slots.
Now, should I connect the monitor to the motherboard video-out or
should I use GPU’s output?
Motherboard output is for integrated video cards.
Suppose the OS (Debian GNU/Linux in this
case) is fully configured to utilize the GPUs i.e. drivers etc. are set
up. Will the graphic system be able to utilize the GPUs irrespective of
where I have connected the monitor?
Yes. Videocard should detect the monitor and report its presence to the video system (X11).
In some cases you would need to configure it manually.
In modern X11 you use your desktop environment UI to configure monitors or you can use the ``xrandr`` tool directly.