As an alternative to modelsim in quartus (there's a free version, but can be a pain to set up) you can use quartus simulator for waveforms that allows relatively straight forward stimulus of inputs - clock, high, low, arbitrary value for buses etc..
Just create a new 'University program VWF' file, add the nodes you want to see and any inputs can be edited for states, transitions, clocks, then 'simulation -> run functional simulation'. Be sure to change the setting in simulation >options to 'Quartus II simulator'. I've been using that and its pretty quick and handy for fairly basic tasks. For qsys stuff I tend to use signaltap II to probe the bus and signals to/from peripherals. It's the only way I could get acustom master to read from the SDRAM controller - by looking at how the NIOS II did it.