Okay... this is how you change the thumbnail.
I put everything (the lrf and the cover image) in the libprs500 folder.
Go to that directory from the command line and type the following
lrf-edit --thumbnail=<filename> <lrf>
so, for instane, if your image was called image.jpg and your lrf nytimes.lrf you'd have
lrf-edit --thumbnail=image.jpg nytimes.lrf
Hope this helps!