Package PLL into User Peripheral

I have a timing critical design needs logic to control PLL, then bring to Nios II level.

RTL level done, but a ghosty feeling haunting. Just like NOT primitive can't be packaged into user peripheral and PLL clken has to be driven by an external pin, I am worrying if PLL can be packaged into user peripheral design.

Anyone has done so, please let me know.

Thanks,