Can I use a the second PCIe slot on a SLI motherboard for...

if the capture card is a PCI-express card. remember, the PCI express standard is compatible throughout the different speeds- meaning you can stick a PCI express x1 card into a x4 or x16 slot, even though it will be physically smaller. and you could [theoretically] stick a x16 card into an x4 slot, even though it wouldnt fit. this is the reason some cheap motherboards have x4 slots that are the size of an x16 slot, but it can only run at x4 speeds.