MyFirstFPGA on Stratix II PCI Express Dev Kit

I can answer one of your questions quickly. For the rest, I am not familiar with that specific board.

Each time you use differential signaling such as LVDS, you need two signals: p and n. Quatrus II will automatically generate the extra signal when you select a diff sig standard. You should always use differential signaling when you can. Make sure however that a differential clock generator is actually used to drive those pins. Look at the schematics and search for those pins and see how they are connected.