What motherboard and CPU do you have?
Intel's modern platforms have some lanes through the CPU and some through the chipset. The CPU's lanes are generally only intended for graphics cards and are dedicated to one or more PCIe x16 slots that are usually capable of either an x16 connection or an x8 connection, depending on configuration. No matter what card you use, be it graphics or not if you use those slots, then you're directly connected to the CPU. A card that isn't a graphics card might not work in those slots if the motherboard's BIOS doesn't support other cards in those slots, such as fairly common PCIe x8 raid controllers.
The other slots, usually PCIe x1 or PCIe x16 slots that are electrically PCIe x4, are through the chipset. These are usually used for non-graphics cards, although many boards do allow for them to support graphics cards if you don't mind a a bit of a bandwidth bottleneck.
Whether or not a card experiences lower performance from having fewer lanes than it is meant to (say a PCIe x8 SSD in a PCIe x4 slot) depends on how much bandwidth it actually uses. An SSD that can use 4GB/s of bandwidth (such as a PCIe 3.0 x4 SSD) will probably be bottlenecked by a PCIe 2.0 x4 slot. This can be avoided by the SSD being a PCIe 3.0 x8 card when it only needs 4GB/s which can be supplied by either a PCIe 3.0 x4 slot or a PCIe 2.0 x8 slot, assuming the x4 slot are physically capable of fitting it (this is usually doable). A card that might be fine with lower bandwidth could be a PCIe x8 raid controller if you're using hard drives on it. That usually won't saturate even PCIe 1.x x8 seeing as you need a lot of hard drives to saturate 2GB/s of bandwidth which could just as easily be supplied by a PCIe 2.0 x4 slot.
Basically, in most motherboards, there isn't some lane splitting chip or anything like that. The slots are physically wired to either the CPU or the chipset, so there's no guesswork involved. Some boards have a chip attached to the CPU's PCIe lanes called a lane splitter (such as Nforce 200, PLX chip, Lucid, and some others) that takes say a PCIe x16 connection from the CPU and can connect to two graphics cards also with PCIe x16. The cards still have the same bandwidth to the CPU, but now they can share it asymmetrically and they can talk to each other directly at full PCIe x16 speed. Crossfire and SLI (especially Crossfire without a bridge) have the graphics cards talking to each other over PCIe a lot, so this helps reduce PCIe bottlenecks of both latency and bandwidth, granted that second one is largely irrelevant since even PCIe 3.0 x4 is enough for most situations.