While it is possible to transfer everything, Windows and GBS and DCS, I'd rather install all from fresh - on a new system.
After installing it, copy the relevant files/folders with settings over. (Though there's a chance your game controllers on the new motherboard's USB ports may require some extra attention ... not sure.
Partitions? One could argue to have Windows on C:-drive, and the rest somewhere else. I have that. But not sure why. Sure, if one needs to re-install Windows, it might make it easier to only format C:-Drive and leave the rest alone. Still, one might need to re-install the rest... I dunno.
Downside of multiple partitions/drives is that you have multiple drives that may run out of free space!