In bios you might be able to assign which pci-e slot is the primary.
You might be able to OC the slots Mhz, not recomended.
Most settings will be done thru the OS, using the cards app.
There are 3rd party apps, as Rivatuner, ATI tray tool. They can adjust cards fan speed or OC them.
Many manufacturers of cards also have secondary apps for stuff. nVidias Precision for example.
OC'ing can ruin a card and a mobo. Stick with the cards app. Surf and read much till you got a handle on it.