To get even close to SATA 3 speeds with a PCI-E card you will need at least an x4 slot. I'm using one in a x4 slot and am getting 380 mb/s with a SATA 3 SSD, so a x1 slot will likely be slower than SATA 2. I did not have to resinstall the OS, I just loaded the drivers, inserted the card, and selected the card in the bios boot order. I am also using PCI-E USB 3.0 cards, and while I have not tested them for speed, they are definitely faster than USB 2.0.
I bought two separate cheap usb 3.0 cards with an internal header (one is HooToo and I forget the other), and they are both working fine.