Thomas, here's a quick outline of steps :
1/ Choose your reset mode
You can start in single-chip mode and then go to expanded mode or go directly into expanded mode using the MOD pins.
2/ Choose the appropriate chip select(s) if needed. The chip selects apply to different addresses in memory so you should choose this in advance of designing the hardware
3/ Design the hardware
4/ In software configure the bus as needed
Size of address and data bus (EBICTL0)
EWAIT and external stretch requirements (EBICTL1)
Decide if the internal flash is enabled (MMCCTL1)
So there really isn't much software configuration required. Have a look at these points and come back if you have any more questions.