I've written a blog post with some information about the Allegiance System. It's not a complete explanation, but covers some important points, including why you should join all four allegiances even if you don't plan to advance in all of them.
http://shadowbanekin.guildlaunch.com/users/blog/2962374/1891258/notes-on-allegiances?gid=165504
Let me know if you find any errors or have any other things you think I should mention.