In Calibre, go to Preferences->Plugins, select the IRex DR 1000 interface plugin, click on the Customize plugin button. A window pops up. De-select epub as the DR doesn't support epub yet. As mobi is now at the top, it will use that as first preference. Then edit the default conversion format as Landrovan suggested.
As to the ebook subdirectory, I had asked about that previously. Apparently there's a security issue where an ebook could un/intentionally overwrite a system file. If you really want that functionality back you'd need to edit the source code. I just learned to deal with it
What I do is create short cuts of books I want to read to the front page so they're easy to find.
Hope that helps.