Hello mountain8848,
1. Reprogram the CPLD with the file config_controller.pof which is in the following directory: nios/examples/vhdl/nios_apex_20k200/ EPM7064_flash_config_controller. You can reprogram your CPLD with this file and the Quartus software.
2. After reprogramming the CPLD you have to config the FPGA with standard_32.sof as described in the Nios Hardware Tutorial (tt_nios_hw_apex_20k200e.pdf) at page 64. The standard_32.sof includes a simple Nios with the GERMS Monitor which should now be ready to program the on-board flash. Please follow the steps described at page 64 exactly.
Bye,
niosIIuser