How do I add hundreds of ebooks to ibooks collection? I usually use Dropbox to get my epub files into iBooks. This works quite well when I only need to add one file at a time, but now I've received a collection of a few hundred epub files.

I am really not used to iTunes, but from what I could gather the collection a book is part of (in iBooks) is not known/registered by iTunes.

If I add all these files to my iTunes library and start syncing to my ipad I fear my iBooks will get completely cluttered with the new files.  And manually sorting the files on the ipad seem like quite a cumbersome task.

How do I conveniently transfer those epub files from my computer onto my ipad straight into its own collection in iBooks?

All the new files can go into the same collection.
You might not be happy with the current functionality of iTunes, but here's how to works. The folder structure from iBooks in iOS doesn't get reflected in iTunes, so you can't control which category new books will arrive in on the device.

You can have a folder of epub files and drag them into iTunes, but they go where iTunes puts them, not a folder of your choosing. This allows bulk injection of hundreds or thousands of books into management for syncing.

The computer version of iTunes will then make a copy of those files in it's Media folder and sync them to all iOS devices the next time they sync (assuming you have the sync rules to sync all Books to each device).

Now, the good news is that if you go ahead and file a book in a category on your iOS device other than Books, that information does sync back to iTunes and the next sync will re-organize things on other devices so you file once, and then sync each device to get them all in sync.

Furthermore, if you have a new iOS device (or erase an existing device) and push all books to that device. The folder status from the last device sync goes to that empty iBooks on iOS.

If and when Apple adds a control to iTunes, you may be able to order books on iTunes just like you can order App icons in iTunes and then sync the device to see the results.