When derive_pll_clocks is run, you'll see an Info message in TimeQuest that shows the exact create_generated_clock commands being run, so that's exactly what is going on under the hood. Just cut-and-paste from those into your .sdc and change the -name option.
(You'll note that the -source option describes the pin going into the PLL, not the top-level port. This is perfectly legal in TimeQuest and gives the same result as if you had used the top-level port(assuming the PLL is driven by the port). The beauty of doing this is the tool doesn't have to know the top-level port, you can change its name or hook it up to something else like the output of another PLL, and the command still works. It's just something that looks "strange" the first time you see it.)