I just checked the specs on it, it looks like the bottom PCI-E lane is a chipset controlled lane, not CPU controlled lane, which means you are freely able to install a PCI-E x1 card in that without impacting your SLI.
Just for future reference, whether or not that bottom PCI-E lane is CPU or chipset controlled is EXTREMELY important for SLI on a Z97 motherboard, because one thing some may not realise is that if that bottom lane is CPU controlled, installing a card in that slot will cause your second PCI-E lane to drop to X4, and when that happens, you won't be able to activate SLI, period. SLI requires ALL cards involved in the SLI to be running at X8 minimum, although XFire have no such limitation. My motherboard's bottom PCI-E lane (Z97-UD5H) for example is CPU controlled, so I cannot actually use that bottom lane at all. From the specs on the manual, it states that the bottom X4 lane also shares lanes with the other 2 PCI-E 2.0 x1 slots, so it looks like it's Chipset controlled, so inserting a card here should not impact your SLI.
AFAIK Chipset lanes and CPU lanes are completely seperate, hence installing cards in Chipset controlled lanes should have no impact on the performance of CPU lanes, though not that it matters much, as GPU's often cannot use anywhere near the bandwidth X8 provides.
However, my opinion with SLI is that if you consider it, you are much better off SLI'ing from the very start, or I wouldn't recommend SLI'ing at all unless your card is double VRAM version or Titan, because one of the limitations of SLI/XFire is that it cannot solve VRAM bottleneck, so it would force you to upgrade your card you were going to SLI in the first place. With an SLI setup straight off the bat, at least you will get the performance of SLI setup from the very beginning.