Hi,
1) Code warrior is IDE. It also contains compiler, linker, debugger and other parts. Code warrior cannot be used for eMIOS code running, but it can be used for compiling and "uploading" the code to the microcontroller.
2) I do not understand this question. What configuration steps you mean?
3) If you want to configure eMIOS for GPIO, you only set appropriate GPIO pin and then set mode in eMIOS unified channel. For example, if you want to use eMIOS unified channel 10 you set:
SIU.PCR[189] - set PA function to eMIOS and set OBE bit
emios.CCR[10] - set MODE bit to GPIO input/output
More information about this mode you find in MPC5676R reference manual (rev.5) chapter 18.4.1.1.1
Regards,
Martin