Hi
Thank your question, mainboard is a big platform to support CPU/GPU/PCH/RAM/HDD/IO...etc. Usually, we will use some stress tool depends on what you want to try .Also we will use different single parts to cross test to confirm it's related to parts... cables or mainboards. For example , I assume VGA card have some issue, but I am not sure it did cause by VGA card, I will use furmark, benchmark to test it . When I found issue, then try the other VGA card to test again.
For motherboard, we have Q-check mechanism inside, if you find error code, your can download user manual to check Q-Code list.