I assume you do have a valid software project, like maybe a hello world or something. Does your software project compile without errors?
The steps are:
1 - Complete your FPGA design using Quartus and SoPC builder.
2 - Provide timing constraints for your FPGA design.
3 - Compile your FPGA design.
4 - Program your FPGA design into the FPGA using the Quartus programmer.
5 - Create a software project and associated system library project using the NIOS II IDE.
6 - Compile your software project in the NIOS II IDE.
7 - Download and Run/Debug your software project to the NIOS II processor running inside your FPGA.
Jake