how to achieve the communication between niosII system and FPGA module

First go to the sopc builder add the desire component like PIO and give it to desire name , and then go to nios-ii processor .v file and add that component in it (take a view of other io, how they are added) and then create new symbol of nios-ii and update it. then you will have that io available at input or output side whatever you select while adding component in sopc. this is the hardware part.