Cyclone V flashing LEDs and clock (Verilog)

I wouldn't try and "read" the code, or other files, generated by the MegaWizard. You only need to know how to put it to use - how to instantiate it in your design. By all means look through the generated files, they're all text files. In several you will find settings for all the parameters you set via the wizard. However, you don't need to necessarily understand them.

Verilog or VHDL - match this to the language you're capturing your design in. Or, are you capturing it as a schematic in Quartus? In which case, on the last 'Summary' tab or the MegaWizard for the PLL, you need to check the *.bsf check box to ensure the appropriate symbol file is generated for you to use in your schematic.

Cheers,

Alex