pcie x1 slots?
I know that you can't run certain things in the PCI express 3.0 slots at x16, like you can run 1 at x16, 2 at x8, etc, but if i plug one thing into a x16 slot and then another thing into the x1 slots, will it limit it the same as running on multiple x16 slots?
Not in most cases. There are some motherboards I've heard of where a x4 slot will operate at x1 if another x1 slot is used or if an integrated device (USB 3.0 or SATA controller) is used, but I haven't heard of any boards doing what you're talking about. However, that does not mean they aren't out there somewhere. It depends entirely on the motherboard designers.
The big thing is that there are a certain number of PCIe lanes and controllers on a CPU and some more on the south bridge. With Haswell processors and the Z87 chipset, that is 16 lanes with 3 controller and 8 lanes with 8 controllers, respectively. So, the motherboard maker could run 3 slots that operate at x8, x4, and x4 from the CPU and run two USB 3.0 controllers, two SATA 6Gb controllers, and 1-4 slots in various configurations from the Z87 chip.
ok so just for clarification, if I, using an ASRock Z87 Fatal1ty Killer mobo (3 PCIE 3.0 x16 slots, 4 PCIE 2.0 x1 slots) were to plug (just for the #'s), 2 graphics cards into the 3.0 slots and 2 USB 3.0 pcie things (http://www.newegg.com/Product/Product.aspx?Item=N82E16815124130), the graphics cards would both run at x8 and the usb 3.0 things would still run at x1?
Actually, with the card you chose there, that wouldn't work. The USB cards are PCIe x4, and wouldn't fit in the x1 slots. In addition, that card model doesn't support UASP on the USB controller.
I would advise this combo:
USB: http://www.newegg.com/Product/Product.aspx?Item=9SIA1JM0S02273 (Just make sure to use the updated drivers. the original drivers suck.)
or if you really need 4 SATA ports: http://www.newegg.com/Product/Product.aspx?Item=N82E16816124064
The SATA and USB controllers on those cards are pretty good since they're newer. The SATA cards won't get you the performance you'd get with the chipset controller, but the quad port one should be pretty close as long as you're using one drive at a time. More than one drive and you'll bottleneck at the slot interface. I think this plan even saves you money.
update: here's the updated driver for that USB card: http://www.techspot.com/drivers/driver/file/information/16820/
ok cool. thanks. And i didn't notice that it said x4...i searched "usb 3.0 pcie" quickly just to have a reference link and grabbed the first that looked like the x1 slot. So what kinds of things can be used through the x1 slots? (aside from wireless receivers, additional USB ports, sata ports or different headers)?
There are many things that work with PCIe x1 slots, from wireless cards to video cards to raid controllers. They're just bandwidth restricted, so don't expect great performance. If you need performance, go with a PCIe x4 or x8 interface, but those are also going to cost a whole lot more. The motherboard and CPU would have to support that, too.