Bookmarks are positions within files that you might frequently want to return to. For example you can use a bookmark to store the location of a interesting part in a recorded interview.
To add a bookmark push Ctrl+B and enter the name of the position. When you want to return to the bookmark push Ctrl+Shift+B to open the bookmark list, select it from the list and select Go to Bookmark in the right click menu.
To select from one bookmark to another bookmark, select that bookmark from the list then select Select to Bookmark option in the right click menu.
Bookmarks (unlike Regions) are linked to an actual file. So they persist even after you close MusicEditorFree or the Project. You should delete bookmarks when they are not needed (using the Ctrl+Shift+B list).
Regions store a selected part of the recording. (A bit like the copy clipboard but you can have many).
To add a region select it, click Ctrl+R and give it a name. Then at any point open the regions list (Ctrl+Shift+R) and use the right click menu to play, select, rename, delete, copy to new or save the region. You can also export the selected region(s) into one folder by selecting "Export Region(s) to folder"
Regions can be extremely useful when working with a long recording like an interview which needs to be rearranged.