It turns out you can use the Assignments Editor to specify a location for a given instance of the PLL. On a new (blank) line, select "location" In the Category column. Use the Node Finder in the "To" column to find the instance. Then in the Value column, select the element type as PLL, which in my case gives two choices: PLL_1 and PLL_2. I found PLL_1 is the useful one.
By the way, the very next sentence following "Depending on the device package, the MAX 10 devices support one or two PLLs—PLL1 only, or PLL1 and PLL3." is "For devices that support two PLLs, you can select which PLL to connect to the ADC." which seems to be incorrect.