Don't use choice #1 - add books from a single directory. Use the drop-down to choose "add books from directories, including subdirectories (One book per directory, assumes each ebook file is the same book in a different format)". Calibre will then assume all the html is a single book, and zip it up in one file. That zip can then be converted into any other of the formats that calibre supports. So far, every mish-mashed html book I've thrown at it it has been able to work out from the internal html code - it knows which file is supposed to follow which file, and where to place images, from links in the code itself.
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