You can download eBook Publisher
here. This software is provided by the manufacturer of the device for converting files to the format used by the reader.
As for extracting the text from your PDFs, it is possible that the publisher of the protected PDFs doesn't allow the text to be copied or extracted. You may have to try to find a way to break the DRM, if you are comfortable with that.
Instead of Adobe Reader, you may want to try PDF Text Reader available for free from
here. I find that it preserves the flow of the text better than Adobe, but you will lose formatting such as italics and bold.
Good luck and don't hesitate to ask more questions.