If your M.2 supports NVMe and you are willing to pay for an NVMe M.2 drive then use the M.2 as your boot and the SATA as storage, it will be about as fast as you can get.
Now if your M.2 is not NVMe then it is no faster than a SATA III so take that into consideration as well. Only advantage is size since most of the time you lose a SATA slot if you use the M.2 as the other poster mentioned. In this case, for me it is easier to use SATA for both or just buy a bigger single SATA SSD.