Where are the jpgs in relationship to the epubs - if they're in the
\media-type\Author\Title folders as
series_index - title - serie - language - author-sort.jpg then try renaming them to cover.jpg and then use the Add Books->one book per folder option.
When your ready a search for "Windows Recursive Rename" will provide links to suitable scripts to do the renaming in bulk, also utilities. If you're not comfortable at the command line try Bulk Rename Utility (BRU), ANT Rename is also good.
I hope you've copied a subset of your mediacentre library for testing. I'd hate to think I might suggest something that would wipe out all you videos, music, books, photos and tax returns
BR