When you enable m.2 mode it disables the 1x pcie slots and drops the bottom slot to 2x giving 2x to the m.2 slot. This is why I've hesitated to use an m.2 drive with this board as I also run a dedicated sound card.
This is taken directly from the owners manual page 1-2 and the table on page 1.26. The z97 chipset is gimped for m2 operation which sucks. Next machine I build will have at least 3 m.2 slots for my boot and primary software drives. Hope this helps.
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