Originally Posted by CyanJustice
...which partitions do I have to wipe exactly, in which order?
You only need to manually format /system when installing other roms, along with the usual factory reset/wipe data stuff. As long as you install a rom after
you format system, the order doesn't matter.
Example, you could format system first then factory reset - the order is irrelevant. What the system format is doing is removing the current system installed on the device (the OS). All a factory reset does is restore the current rom to basic factory settings - it doesn't erase anything in terms of the OS.
That's why formatting /system (especially when changing bases) is so important; it prepares the device for the new rom you install by allowing a clean install every time.