The library I use has Mobipocket books and Adobe PDF books. All of the books are DRM protected. I usually check out Mobipocket books because I can read them on my Cybook Gen3. If I check out Adobe PDF books, I can read them on my computer or my pocket pc because I have been able to activate those devices through Adobe's website.
I imagine most libraries use the same, if not identical, technology for electronic books. Perhaps this link can help you out:
Adobe PDF Library Books (The Seattle Public Library)
If you have a regular, unprotected PDF file, you probably can convert the file to a format that could be used on your eBookwise reader, but you probably won't be able to get very far with the PDF DRM encrypted library books.