Those old Intel chipsets didn't have native pcie 3.0 or usb 3.0 support so it had to be added via the available pcie 1.0/2.0 ports. To make matters worse the P55 PCH (southbridge) only had pcie gen1 (250 MBs) ports.
It was quite a mess and these solutions came in various forms. (This got pretty long, skip to the TL;DR if you just want to know what you can do with that board.)
Some added a bridge chip that bridged 4 PCIe gen1 (250 MB/s each) lanes from the PCH (southbridge) to several single gen2 (500 MB/s) lanes for things like USB 3.0, SATA 3.0 controllers and PCIe 2.0 slots. Higher boards like the P7P55D-E Pro and Deluxe had this (I paid extra for a pro to get this features). The result is that you could get 500 MB/s from these ports/controllers, at least until you tried to use more than 2 of them at a time and maxed out the 1GB/s bridge chip to PCH connection (pretty rare I think, even a file transfer between them would only go from one to the other). (There is also only a 2 GB/s link between the PCH and CPU but it shouldn't be a bottleneck given the 1 GB/s bridge chip link).
Lower end boards had various ways of connecting these controllers either to the PCH gen1 lanes or the gen2 lanes on the CPU (of which there are only 16, so they need to be 'stolen/borrowed' from the PCIe x16 graphics link).
The most basic (and worst performing) just connected the SATA/USB 3.0 controllers directly to single gen1 lanes. That makes the SATA 3.0 completely pointless by limiting it to 250 MB/s (across all ports!) when even the native SATA 2.0 ports on the chipset have have 300 MB/s each. The USB 3.0 is also crippled but 250 MB/s is still several times faster than USB 2.0 (but only about half the speed USB 3.0 is capable of).
This page compares the two solutions I've detailed so far, the bridge chip and just using the gen1 PCH lames. »www.tweaktown.com/articles/3079/ ··· ex2.html
Finally they could appropriate some PCIe 2.0 lanes from the 16 on the CPU that were meant for graphics. The weak part about this is that as soon as you take even 1 or 2 lanes, the graphics link has to drop from x16 to x8 since numbers in between aren't supported. However x8 is still pretty fast, apparently even a 5870 is not hurt much by this so unless you have a faster card than that it shouldn't be a problem. I suppose how they use those 8 lanes varied, but I imagine the typical use would be to use one 500 MB/s lane for each of the USB 3.0 and SATA 3.0 controllers. In that case performance would be similar to the bridge chip solutions above.
That P7P55D-E LX seems to be an interesting case, where you can choose to use either gen1 PCH lanes or gen2 CPU lanes using an 'IO level up' switch or the BIOS. However it seems you can only choose either USB 3.0 or SATA 3.0 to be hooked up to a gen2 lane?
TL;DR This is a value board so it doesn't have the high-end bridge chip that would let you have 500 MB/s for each of SATA 3.0 and USB 3.0 as well as x16 graphics. Instead you get to choose which one you would like to fast according to the IO level up setting:
[disabled] x16 graphics, 250 MB/s USB 3.0, 250 MB/s SATA 3.0
[USB 3.0] x8 graphics, 500 MB/s USB 3.0, 250 MB/s SATA 3.0
[sATA 6G] x8 graphics, 250 MB/s USB 3.0, 500 MB/s SATA 3.0