How to feed external clock generated by PLL into SOPC system?

very possible

1) in sopc builder under clock settings add as many clocks as you need and make sure the sources are set to external. On the far right specify the frequency you need in Mhz for each clock.

2) generate your sopc system and place it on your project's top bdf file , you'll see inputs at the top left for all your clocks specified in the sopc builder.

3)start the megawizard plugin manager and create your pll with the desired clock outputs, when done place it on the top bdf of your project

4) connect, wire the outputs of pll to clock inputs of sopc builder