Why are there humps in my ATX case where I mount my Motherboard?

Are these humps built in Risers, so I dont need to add any? Because I added Risers to the humps but now my motherboard does not match up with the I/O panel it came with. And also now my Pci slots dont match up with the expansion slots on the back of my computer. My tower is a xion onyx and My motherboard is a gigabyte ep45-ud3p. what should I do. Pleas help!!!!!!!