I am a little confused by what you said. It sounds like you can run individual software using the picker but can't see the directory list. If that is the case you need to set the default software directory.
In one of the menus there is a Directories option, then select software from pulldown menu and add the folder that you have your files in.
If you have all the system folders named the same as the systems you just have to do this once. a2600, snes, nes etc...inside your "software" folder
that what you needed?