It outputs the manga into a series of jpeg pics that are in order and fit to the Kindle's screen. Each jpeg is like the "page" of a book. There is also two smaller files included that allow the Kindle to "read" the jpegs like a book and remember your place.
Mangle outputs the jpeg files in a single folder. Just drag that folder to your Kindle/SD card and it will show up in your book list. Then just read like a normal ebook, turning the pages normally.