First, Manichean knows what he's talking about -- listen to him.
Also, I'm basing my comments on my Sony 505, which I believe is substantially similar to the 650 (though, lacking a touch screen, it's immune to Cheeto-dust-covered fingers).
I'm a little unclear on why you don't want collections. Most of the time, people who don't use them just ignore that option; it's the people who
do use them who get worked up about their type and number. Either way you're going to have the "collections" item (an on-screen button on the 650?) visible, just with 0 items if you have no collections defined, so if you're not using them, going to a lot of work to make them go away isn't really saving you any screen real estate or anything. If you prefer to access your books by title, author, etc., the presence or absence of any number of collections doesn't change those.
Collections are automatically created based on tags, series, etc. (I've forgotten what the default is because I've had mine customized, and not touched it since, for a year or two) You can turn off this functionality completely, or you can set it to what you want your collections to be. Personally, I find collections to be very useful. I have a couple of thousand ebooks on my 505, and it's handy to be able to find all the SF, for instance, or all the tech manuals, without having to remember a manual author's name or digging through all the authors starting with a given letter. But if you don't, there's a setting to shut it off -- I'll need to check calibre itself if you really need that.
By and large, it's a good idea
not to delete books from your calibre library. Ebooks are not just small but tiny, so having them on your computer doesn't take much space. With them in your library, you can fix their metadata the way you like it, organize them in proper series when appropriate, tag them to make them easy to find and organize, and so on. And, of course, if you need to re-upload them to your reader for any reason -- you want to change something, perhaps, or for some reason you had to do a hard format -- there they are, ready to go.
Does that message really say "friles"? If that was a direct cut-and-paste, I think something needs fixed. *snicker*
To expand on what Manichean said, you can and should copy the books back to your computer by connecting your Reader, viewing the books on it (clicking the reader icon on the toolbar), selecting them all, and right-clicking for a copy option. However, these will go back into the directories that calibre establishes,
not "one directory". Read the sticky in this section about changing the calibre library folders and why you can't. Calibre's internal folders are its business, and you should treat its innards like a black box -- or a database, which is what it behaves like -- and interact with the books only via the calibre GUI. That's what "save to disk" is for, by the way: I keep insisting it should be named "export" for clarity, because it acts like a database export function and saves books wherever you need them, so that you could do something like pack up all the Harvard Classics and send them off to a friend.
The "copy to clipboard" button copies
the error message to the clipboard. It may seem a bit silly for some things, but it's part of calibre's standard error message dialog box, and when you have something long and complicated (a big error explosion, for instance) that you need to post here you'll really appreciate it. The rest of the time, just ignore it.
Like you, I started with the Sony software and discovered calibre. It's one sweet program. I've watched it grow over the past year+ and it's just amazing.
Read my .sig (well, the post linked in it), specifically the part about how calibre manages books, not files. As a new calibre user, that was the hardest thing for me to wrap my mind around; once I internalized that, everything else suddenly made perfect sense.