It's possible to modify vhdl in quartus with out to close ModelSIm

so you are using NativeLink to start an RTL simulation? if so, you can edit the source HDL and re-run the .do script (one way is to push Up in the transcript window until you see the Quartus generated .do file and then push Enter) in ModelSim without going back to Quartus. if you've added signals and re-run the simulation you can also push Up then Enter to re-run those commands. you can do this as long as you haven't added/removed HDL files to your project, if you have you'll need to re-run NativeLink

alternatively you can copy+paste the add wave commands from the transcript window into the Quartus generated .do file, then re-run the .do file using Up then Enter. you can even tell NativeLink to launch ModelSim using your edited script. the downside is that if you add/remove source files you have to add them to your edited .do file yourself, or re-run NativeLink to generate a new .do file, then add your custom wave commands back in

i should make an AlteraWiki page with some ModelSim tips