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Recommendation: maintain your own SDC file and don't let TimeQuest overwrite it. Timeuest's outputs have horrible style.
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Expanding on that important point...
None of the following specifically addresses your original questions, but I wanted to cover this here since Randall brought up the write_sdc issue.
do not use write_sdc to overwrite your .sdc file. That's not what the command was meant for (even if you see it used that way in examples or tutorials). If you are starting off creating constraints in the GUI, then you might want to use write_sdc to create your initial .sdc file, but you will still get that "horrible style". More likely, you will want to copy the constraints you entered in the GUI (whether by typing in the Console or through dialog boxes) to the .sdc file you are creating yourself.
Rather than as a means to create an .sdc file you will subsequently use as an input to TimeQuest, think of write_sdc more as a way to see how TimeQuest is interpreting your constraints (how it is expanding wildcards, how it is converting derive_pll_clocks to generated clocks, etc.). If you just want to see how your constraints were interpreted, you will probably prefer "Report SDC" under "Tasks --> Reports" in the GUI. The result will be listed at "Report --> SDC Assignments".
When copying GUI-entered constraints to your .sdc file, copying them one by one from the Console has the advantage that you'll notice any warnings for problem constraints. If you've entered a lot of constraints, you can right click in the History tab and do "Save to File" to get them all at once in a form that makes it easy to copy to your .sdc file without having to strip out the extra Console lines. The History tab just won't flag the constraints where TimeQuest already found problems.
Even if you like to create your constraints in the GUI instead of typing them from scratch, give the SDC File Editor in TimeQuest a try. (Use version 7.1 to get the latest enhancements.) You can still use the dialog boxes like "Set Input Delay" from within this special text editor to create the constraints instead of typing them; the dialog boxes copy the constraint to the file automatically. After an SDC command is in the file, hover the mouse over the command to see a tooltip showing the command syntax. (The Quartus file editor will give you Tcl color coding for things like comments, but it won't create SDC constraints for you or display SDC tooltips.)
By the way, that History tab is also a good way to create the starting point for a Tcl script that does all the steps like project_open, create_timing_netlist, read_sdc, etc. After you have a script in the project directory, it will be listed on the "Script" pull-down menu where you can run it easily.
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