Play with it.
It will creat what ever File / Directory structure you want.
As for taking longer - yes it can, again play with it, maybe you have some very rigrious ripping settings - EAC can be set up to try it best to ensure a perfect[/] rip. Also the Lame setting provided is a High Quality one which will take time (~2x-3x on my P3-700),

Again spend time on research before you rip your CD collection - nothing worse then having to redo it all.