Not sure what issue you are having... but as a general rule I always recommend using the LMCE folder structure, but that is only so that you have the Filename sort option in the media grids.
If you do not use that option, then all your media needs to be tagged with meta data before it will appear in the other sort modes (eg Title, Performer, etc) Any audio you have ripped from the source using a decent ripping program, to mp3, will generally have this meta data downloaded from the Internet and written into the embedded id3 tags inside the mp3 file.... LMCE will read those in and use them as the meta data so that you can see the media. Well known DVD's ripped on LMCE itself will also be tagged by LMCE (but not if you rip the DVD's elsewhere). Even mp3's downloaded from the Internet generally have their id3 tags already set ready for LMCE. Almost all other media have no meta data, and so needs to be added through the LMCE admin interface before they are visible in the media grids with those other sort modes. Using the LMCE folder structure, when asked during detection of your shares, will give you the option of browsing your media under the Filename sort mode, irrespective of whether they are tagged, because it is just using the file/folder names to display the media.