From my investigations I think that the Internal/Books/Mobipocket folder is where the Mobipocket desktop software will put books. I deleted it on my iLiad and it automagically reappeared when I next rebooted!
All the Mobipocket format books I have get put into a dircetory (of the same name) with the prc file and a manifext.xml in the directory when they are first opened.
The manifest file allows the iLiad to store the name of the book and author in a file that is much quicker to read than the prc. I believe it also stores your current position and reader settings for that book in the manifest file. Also, for fun, if you have a cover image for the book, put it in the same directory and edit the manifest.xml file to add an <image> tag in the <y-metadata> section like this:
<package> <metadata>
<dc-metadata>
... stuff ...
</dc-metadata>
<y-metadata>
<image>filename.png</image>
... more stuff ...
</y-metadata>
</metadata>
<directory>
<content>.</content>
</directory>
This will then use the specified image for the icon in content lister.