If you do not have enough logic to probe with SignalTap, then build a modelsim simulation. Its possible that the default Modelsim simulation that Quartus will create will be sufficient for you. In SOPC Builder check the box that creates the simulation files, and then click generate to regenerate the SOPC system and the simulation files. For an SOPC system called sopc_system.sopc, the simulation folder will be called sopc_system_sim/. Inside that folder is a setup_sim.do file. Start Modelsim, cd to that directory, then type 'do setup_sim.do' at the Modelsim command line. Read the text instructions that you see, eg., type 's' to synthesize the design files. I think there is another command to add default signals to the wave editor, alternatively type 'add wave *' to add the top-level files. Then type 'run 10 us' to run the simulation for 10 us.
Look at the reset signal and your top-level I/Os that you are having trouble with.
If none of this makes sense, then you need to do some more reading. There is an application note regarding debugging NIOS systems using Modelsim.
http://www.altera.com/literature/an/an351.pdf Cheers,
Dave