Not too much difference between the two factions, mainly cosmetic and their PvE maps differ. Alliance Battle maps depend on which side is pushing which back with their faction counts.
You don't need to do much to take a side, just have more Factions points from one side than the other. To align a guild to a faction, just get to Cavalon (Luxon town) or House zu Heltzer (Kurzick) and talk to their ambassadors.
