I don't have a premium account, but for now some observations.
The settings are very simple, you can select one notebook for downloading and one for uploading, you can download all evernote clearly articles and let evernote sync automatically (but only if you completely shutdown the device, which takes relatively long).
If you want to upload quotes you can mark a certain text, and with options like adding notes, you have an option to send it to evernote. I did not use this, but I think a new note is created in the upload notebook.
The other option is downloading all notes in one article. My layout there is not really strange, so did not notice strange stuff while reading. The notes or drawings made are not synced with your account and at the moment you can only delete articles from the selected download notebook. The articles you view in other notebooks, but which are created in evernote cleary, can not be deleted on the reader.
I did not test the speed of 1000 articles, but I can remember I once downloaded 100 articles and it took I think more than 5 minutes. So I suppose 1000 is quote a problem for the device.
Also I didn't find an option to send drawings or created notes on the reader.
For now my main use is reading some web articles and especially a way to read some interesting RSS articles, which I select in Google Reader that I want to read them later. For the rest I think I lot can be improved to do a lot more with your notes.