Option 1: make a shell script containing a line for each book you want to convert. Choosing input and output file names are easy.
Option 2: make a shell script that loops over its arguments one by one, converting each book. Use shell tools like 'basename' to construct the output paths.
Option 3: make a shell script that uses 'find' to walk a directory tree, converting books as it finds them. Again, use various tools to construct the output path.
Option 4: make a GUI widget that accepts drag & drop, then processes each file one at a time.
Option 5: some other way to do it.