antonypace, there are two IDEs. The "newer" one is based on NiosII Build Tools which gives the user full control over the build process. You can provide your own Makefile, you can use scripts to generate this or you can use the BSP settings editor. In my Windows installation this IDE is located under:
C:\altera\91\nios2eds\bin\eclipse-nios2.exe Actually (version 9.1 SP1) this IDE has a bug. When you want debug through user libraries source code is not displayed. (SR10752121 , will fixed probably in 10.0)
The "old" IDE uses automatic generated Makefiles. All settings are derived from the System Library Properties.
The installation path is:
C:\altera\91\nios2eds\bin\eclipse\nios2-ide.exe Jens