question about pcie and ddr2 in nios ii

I connect pcie x4 and ddr2 control modual to nios.but when the generation finished, I found that there are so many port . the pcie x4 port what I needed just the : refclk,serdes in[3:0],serdes out[3:0].but there are other port like : gxb_powerdown_pcie,pipe_mode_pcie,rxdatak_ext_pcie,rxelecidle_pcie,and so on.Is that means that I must write some moduals to reset the pcie core or control and monitor it's working status .Is that true?Is there example code about the pcie of nios ii,thanks!