PCI Slots and PCIE

Hey all new here looking for answers!!

Ok have a fairly descent gaming pc and i did have SLI but got rid of 1 gfx card to connect a firewire/usb pci card (small port) but now thats blocking my graphics card fan and is over heating i have 3 graphic card slots and when i put 1 graphics card in the middle slot it says i cant do this and should move it to the 1st slots its really annoying can any one give me tips or explain why i have 3 slots and can only use 1 for 1 graphics card i know its for SLI but it should be able to take a graphics card.

Mobo: Nvidia 780i SLI
RAM: 2.5gb
Gfx: 8800GT 1gb

Thanks all - TMM