Cyclone® IV GX devices have two types of PLLs - multi-purpose PLL (MPLL) and general purpose PLL (GPLL). The Quartus® II software will automatically select the PLL type based on device usage and resources.
If you wish to specify a particular PLL to be used in your design, you can use the Assignment Editor and add location assignments to your PLL instances. The syntax for the location value would be PLL_1, PLL_2, etc.
The .qsf syntax to assign a PLL instance to location PLL_1 is:
set_location_assignment PLL_1 -to "<instance name>:inst|altpll:altpll_component"
Refer to Clock Networks and PLLs in Cyclone IV Devices (PDF) to understand which PLL numbers correspond to MPLLs and GPLLs in your device.