And yes, most motherboards have a "primary" slot where it's a real x16 slot, and 1 or 2 or more SLI or Crossfire slots which are x8 or even x4.
Actually, most motherboards today have auto-switching slots, so that they have 16 lanes assigned to 3 slots, and the motherboard and card negotiate so that each card performs as fast as it can regardless of slot, up to the total maximum of 16 lanes across the three slots. This means there is no "primary" slot any more, and helps you lay out cards where clearance is an issue.
What this means is that you can install that x16 video card in any of the three x16 form factor slots, and it will get all 16 lanes. If you install a card in another of the x16 form factor slots, it will get up x8 if it asks for it, and the first card will be dropped down to x8 as well. Install a third card, and you end up with x8/x4/x4, but again, no slot is "primary".