When capturing a schematic with Altera® FPGAs, you can use the Pin Connection Guidelines (PCGs) to understand the board level connection of the device you are using. Currently, PCGs are available for the following Altera devices: Stratix® IV, Stratix III, Stratix II GX (which can also be used for Stratix II devices excluding the transceiver portion), Cyclone® III, Arria® II GX, and Arria GX.
The PCGs are also a useful tool for schematic reviews and pinout reviews of your design.
These guidelines are found in the Literature Page under Pin Connection Guidelines. A link to the PCGs is also found in the Device Pinouts page for the supported device families.
You can also find PCGs for the Altera FPGAs by performing a search for "PCG".