Hi Cyndessa,
I'm not sure I understand completely what you are asking. It sounds like you maybe have annotation extraction figured out; you certainly have the right link, so let us know if you have any problems with that process. If you haven't tried extracting annotated ebooks from your EB1150 yet, remember that this process will only work for books that are on a memory card (accessed via a card reader), and not for books that are on the EB1150's internal memory. As for your question--"I am not sure if this is the full .imp file for the ebook or just for the markups"--the reimped .imp file will contain both the entire text of the ebook and your annotations. It's really slick.
But is your primary concern converting books to other formats? If so, your mileage will vary. If you want something that will preserve your annotations, I don't think it exists. I wish it did. If you just want to preserve copies of the unannotated books, you can extract text from imp files. I've never tried the IMP GUI Converter, but I know nrapallo has
a tool for extracting text without formatting here. But the loss of formatting is a bummer. Is the IMP GUI Converter able to retain images and formatting? If so, I would save the converted books as html if that is an available option. In fact, html is easily convertable into any conceivable ebook format (EB1150 included), and so it would be a good choice for your library in the long term. The problem is, most commercial ebooks are not available in html format, so if you want a scalable library of modern, copyrighted ebooks, you will probably have to buy a more popular format and then de-DRM and convert for whatever device you happen to be using. This of course brings up legal concerns (we cannot tell how to de-DRM on Mobileread, for example). And none of this helps if what you are after is conversion of annotated .imp files.
Does this answer your questions? Partly at least?