OK, I'm going to try to glaze over the big points. If I go too deep my apologies.
The Intel chips have a certain amount of interconnectivity, in the form of PCI-e lanes, available to them. Some of these lanes come from the PCH (Platform Control Hub, the device that talks to the CPU), while others come from the CPU directly.
This limited number of lanes can be assigned to any number of slots. A board with 32 PCI-e x1 slots and a board with 2 PCI-e x16 slots can be made from the same CPU/PCH combination.
When a manufacturer advertises that a board will run in x16/x16 with two slots populated and x16/x8/x8 with three slots they are saying that the available 32 lanes can be divided multiple ways, but there are only 32 lanes available.
Given what you're stating, there should be no problem populating any of the slots. The graphics card, a x16, should go into the primary slot. Check your motherboard manufacturer for which one to populate. Any subsequent, non-graphics, cards can go anywhere. The fact that you aren't currently running multiple graphics cards means that there should be little concern in populating any other slots.
Edit:
Motherboards generally have a set list of where to check for a specific piece of hardware. That's the reason manufacturers generally tell you where to put a graphics card (check the motherboard manual, available online if you don't have a paper copy). They can work with graphics cards in other slots, but are generally rather finicky about wanting to do this. In short, putting the graphics card in another slot might be possible, but it definitely isn't recommended.