jtag debugger dosen't finds the connected cyclon ll processor

What do you mean program the controller? The Cyclone 2 is an FPGA , the NIOS II is a soft core processor. So, you've used the NIOS processor and built an SoC kind of subsystem in the FPGA. The FPGA programming is also successful. When you say controller are you referring to the Software for the NIOS subsystem? If so, then you have some issue with the SW that you've written for the NIOS. I'd suggest you check the HW design for correctness, then verify that you've initialized the NIOS in the EDS correctly. If all is done correctly, the NIOS should boot and run your code.