Am I Screwed? PCI Vs PCI Express

So the motherboard I ordered has 3 PCI Slots and 3 PCI Express Slots. All of the rigs I see pictures of seem to have each GPU on a PCI Express. I bought a metal rack as my rig and planned to zip tie all of the cards over the motherboard and power supply. I bought one of the 6 PCI Express risers packages.

I guess worst case scenario I could have 3 cards running on the motherboard on the PCI Ports and have 3 of them hung above everything on the PCI express ports.

Did I make a mistake by buying this motherboard. I researched a few motherboards and could only find ones that have 5 PCI Express slots.

Besides having 3 GPU's near each other on the motherboard and probably not being as cool, is there any real downside to running 3 of them on the PCI Slots?

Also, Can I plug the PCI Express risers into the PCI slot, or is that a no go. Sorry for the noob question, thanks for the help.