Design/Simulation flow question

I want to save my waveform settings (radices, which ones are displayed, dividers), but I also want to automatically generate my ModelSim project from within Quartus II (from within Tools -> Run EDA Simulation Tool -> RTL). So far, the only way I can do this is to manually create a .do file.

Is there a better way to achieve this design flow? I'm also looking for any recommendation on a design flow tutorial.