Have you explored the features of the Calibre Companion app? (Available via GP store.) It might help you do what you want.
- It seems to "wrap up" the cover and book into one zipped file which are all in one directory. Downside is that they are given gibberishy names, so you have to go through the app to remove things.
- If you have a lot to sideload, create "tags" in calibre. These in turn can be used as "shelves" on your device thru the app.
- Dont have to physically connect your device to your pc (which is a boon for those of us having issues with the mpt protocol.)
Many of the posts on calibre and calibre companion have been tagged already. (Go up to main HD/HD+ forum, look on the right hand side for TopTags -you have to scroll down a bit - and select the tags. It will bring up a list of threads on these topics.)
Calibre does create all those folders for each book, but I have mine set to be stored on my pc. The problem may be coming from the way that you are transferring the books over to the Nook. In Calibre, right click the title you want to send to device. Do NOT choose from the top options.
Go down to "send specific format to." Then choose from the options of where to send it. When you click that, a "choose format" window opens. Choose what format you want and only those files will be transferred to the Nook. It is the easiest way to get the books on the Nook.