Take a look at the configuration chapter in volume 2 of the Cyclone II handbook. You will need either a download cable or a configuration device of some sort EPC, flash with controller, flash with microprocessor. Download cable like USB Blaster can be used to program in Passive Serial mode and also JTAG if the device is in a JTAG chain. I think you will find the information you are looking for in this chapter linked below.
http://www.altera.com/literature/hb/cyc2/cyc2_cii51013.pdf (
http://www.altera.com/literature/hb/cyc2/cyc2_cii51013.pdf)