Simulate with Altera IP in ModelSim

In principle you compile any source code into a chosen library which defaults to work. Then you simulate any level by selecting from work.

you will then need to add waveform file by choosing your inputs and applying logic.

Ideally a testbench can be used to inject data into top level.

When you compile, check what is the default library.

The nativelink is not a separate simulator but it launches modelsim from quartus (ready for your design), I never use it.

Many designers use tcl or do file to compile and run simulation at a single click.