NERO and Alliance rules share the same roots, but they have evolved into very different and separate systems at this point. So you might see some of the names of spells are still the same, and the basic style of combat I think is pretty much the same, but there are classes we have that they don't, they have some skills and spells that we do not, etc. The systems are not interchangeable, and a character cannot transfer from NERO into Alliance or vice versa. A person can play both games if they like but you must have separate characters in each game.
Alliance uses a land called Fortannis, but each chapter has its own lands with different settings. These continents are separated by a magical mist that will allow individuals or small groups to travel to and from various lands (so players can play at any chapter they like, but you won't see inter-chapter wars because no huge armies can get through).
For example, the HQ campaign is based in a kingdom called Icenia, which of course is surrounded by other countries - some allies, some enemies. The Connecticut campaign is set in Caldaria, Ohio is Vandlar etc. The plot committees of each chapter can create a world for their players within Fortannis, but all use the same rules. One chapter might have its home kingdom set in a sea-faring kingdom. Another might be set in a desert; yet another could be recovering from a devastating war and be almost post-apocalyptic. The plot teams can be creative in building these worlds, but they are all connected.
Hope that helps paint a clearer picture of the style of game we use.