infrared

So Cyclone II is a good start. I assume you are using a demo board. The only board with Cyclone II and IR that I know of is the DE2 Terasic board: http://www.mouser.com/pdfdocs/terasic_de2_usermanual_16.pdf

This will refer you to microchip's paper: http://www.microchip.com/stellent/groups/sitecomm_sg/documents/training_tutorials/en532270.pdf

Based on this paper, it looks that the IR sensor is interfaced to the FPGA via a UART handler (MCP215X). So this is good because you only have to worry about the UART. They say the baudrate is 115200.

So all you need to do is go to Qsys, drop in NIOS ii cpu and UART RS-232 IP. Expose UART-RX and TX. Then write the communication protocol in NIOS using C.

Here is a very good link with code to use UARTs with interrupts: http://www.alteraforum.com/forum/showthread.php?t=17224

Please confirm which board you are actually using. FPGA development is not easy so keep at it!