Actually you want to go to the Nios II command line and compile from there. The software projects use the new command line tools. You should be able to go into the software project folder and type "make" to compile any of the software projects.
It's possible to use the Nios II IDE to compile the projects but just as a heads up with the C2H Mandelbrot design, the hardware accelerators are already present in the system. In order for them to be targeted by software properly you might need to "re-accelerate" them which means you would have to recompile the hardware project.