Did you watch the all training videos to help you learn how it works? Yes, it is a bit complicated, but then so is Rolemaster many gamers say, and as a user I think ERA does a remarkably good job, and I am very happy with the level to which I can modify things and get it to do what I want. It takes time to learn it, and that was impossible until I watched all the videos, and in some cases more than once and in slow-mo. I for one am very happy that I spent my money on it, and have devoted weeks to understanding, using and modifying it.
To save a character, you click on the "Server" button next to "Save" (because it uses a client-server implementation, and you are saving it to your server). If you click "File", you can save it out to a separate file name. It's all in the videos.