Which version do I use?

For Stratix support you pretty much need the subscription edition. Since your are a student, you may be able to work with your school and use their license. I don't know if there's a student licensing deal or not, but if they are working with the larger devices they should have a license.

As far as the waveform editor, I suggest using modelsim Altera Starter Edition, (which is included with the subscription of Quartus). This is not the old waveform editor simulation that was built into quartus, but it's more of an industry standard simulator, that you should learn how to use.

Pete