Problems with Cyclone III - NIOS II Embedded Evaluation kit

The warnings in Quartus are no problem.

Have you installed the usb-driver?

Have you created a new project? Or only oppened the .c File?

Here is the Link to the Altera driver information

http://www.altera.com/support/software/drivers/dri-index.html

Can you download the design into the FPGA with Quartus Programmer?

In the NIOS IDE start a new Project C/C++ Application. In the next dialog you can choose the sample applications (count_binary template) and you have to choose your Quartus hardware design, which should be used for this software. Click finish and the project will be created.

Now right-click on count_binary and choose in the opened menu System Library Properties

and only activate Programm never exits and Small C Library.

That's all. Now you can build your project.

Download the hardware design into the FPGA and than Choose Run<Run Hardware.

http://www.altera.com/literature/tt/tt_nios2_hardware_tutorial.pdf

I think this tutorial can help you to run the sample application.