You don't use Book formats and folders to choose a reader app. That is used to choose the folder on your device where CC is to put the books.
I am not a Mantano user, but I have tested CC with Mantano Lite. It doesn't seem to care what folder you use, so you probably don't need to change the default unless you don't want to use CC as your library organizer.
If you use CC as your organizer, then you can use it to select books and launch Mantano. In CC, tap on the book you want to read to open Book Details, then tap "Read" to open the reader app. If you have only one, then that app will be opened. If you have several, then you will get a dialog asking you which one to use. Alternatively you can long-tap on a book to open the reader, avoiding the book details display.
If you want to use Mantano as your organizer, then I think the best thing to do is tell Mantano to get the books from CC's folder. I think that the following will work. Go to Mantano's settings, choose "Bookshelf", then "Import Folders", and "Add Folder". Tap the box next to "Calibre Companion", then the "Add" button. You will probably need to use Mantano's import feature to actually load your books into Mantano.
Personally, I wouldn't bother with all the import stuff, instead using CC to launch Mantano. But I admit that I am a bit biased.