Run through these two example designs;
Post#2: de0_nano_basic.zip
http://www.alteraforum.com/forum/showthread.php?t=39765 Post#2: de0_nano_sdram.zip
http://www.alteraforum.com/forum/showthread.php?t=45927 This example contains a Qsys system and uses GPIO, so will have features similar to what you are looking for.
In your case, where you want to communicate with a DDS, you will need to determine what the DDS interface protocol is, eg., is it a serial interface like SPI, or is it a parallel interface. If you have a part number, I can look at the data sheet and comment on what you would need to do.
Cheers,
Dave