You need to understand that the motherboard is the link to every single hardware inside your computer. This means that it will need to be compatible with every piece.
1st - CPU socket. You need to chose your mobo in order to fit either your AMD or Intel CPU, plus the type of socket (FM3, FM2+, 2011, 1550, etc)
2nd - GPU. Is your GPU DDR5? PCIe? You need to know those things in order to make it work.
3rd - Eveything else. Less important, because of backward compatibilities, but still. HDD (SATA, IDE, etc), RAM (dual channel, quad channel, speed in Mhz, etc)
A good place to start when searching for compatibility issues is here : pcpartpicker.com
This site helps you with compatibility filters.
Hope this helps!