This is possible by applying constraints in the Assignment Editor.
 
The setting method is shown below.
 
1. Start Assignment Editor
2. Register the input data you want to synchronize in the To column
3. Select "PLL Compensation" in the Assignment Name field
4. Select "On" in the Value field
5. Select "Yes" in the Enable field
 
After compiling, from Fitter ⇒ Resource Section in the compilation report,
Select PLL Summary and check if the pins registered in Compensated inut/outpu pins are assigned in the corresponding PLL.
 
Devices that support this feature are listed below.
Arria II GX, Arria GX, Cyclone II, Cyclone III, Cyclone IV, HardCopy series, Stratix series