1. open a "command prompt" (or Start -> Run, enter "cmd" and click "Run")
2. change directory to where you installed the NIOS II, subdirectory "bin\eclipse". In my case, this means "C:\Altera\Kits\NIOSII\bin\eclipse\"
3. run Eclipse (which is called "nios2-ide.exe " here) in "clean" mode ("nios2-ide.exe -clean").
4. enter the location of your workspace, allow the program to start, and check that you can see the Mocrotronix options under "New". Go: New -> Other and expand the Linux tree.
5. close the IDE and the command prompt window.