Your motherboard will fit in the case since both of them have standardized mounting holes, all you need to do is match the correct hole of the mobo with the correct holes in the case and put the mounting screws in.
Since you have more free space in the case, I think it's better since you can get a lot of better cable management and much better air flow and cooling.
It's also a plus since it gives you more options for upgrades in the future and more free space for anything else that you plan to plug in later, also free space is easier to keep clean and neat....