Dynamic counter values for PLL

You can dynamically reconfigure the PLLs, and there is an app note describing it. But note that M, N and P are just high-level representations of SRAM bits in the device, and the Quartus II software has to translate those values to what the SRAM bits. So there's nothing like that on-die, i.e. you won't be feeding the PLL these high-level parameters, you'll be feeding it configuration bits. The app note will explain it better.