Hi,
You may refer to the Stratix ii handbook for more information regarding configuration scheme, pin guidelines, remote update..
https://cdrdv2-public.intel.com/654261/stratix2_handbook.pdf
If you're using AS configuration, you will be limited to remote updates, meaning the FPGA's configuration must come from an external source, typically managed remotely or from a remote control system this is because in the Active Serial configuration mode, the FPGA’s configuration is typically loaded from an external device (like a serial Flash memory).
Regards,
Aiman