Over the time I use eagle many things are complicated. There are things I don't like in the User Interface. But luckily you can customize the UI a little bit. Sadly, it is not really easy, because you need to edit a script if you want to have additionally buttons. I also need to make my own Images for the buttons.
Lets start with the Folder. I like to use my own project folder "workspace" where I always have my currently working projects. These can be a lot. It is easy to change the path. Open the Control Panel, then click on the menu Options, then Folder (or Directories).
I have a special folder for my libraries, because I don't want to mix them with the original one. The directory which is first in a line will also displayed first in the control panel. Because I often need access to my libraries this is very helpful.