In most cases, you can! Keep in mind that each ebook platform (Ebook Central, EBSCO, etc.) works differently, and so the process for highlighting or annotating ebooks will vary.
In EBSCO, for instance, you'll first need to set up a free My EBSCOhost account. Then, you can save a book to your folder and make notes in it. To see them later, you'll sign back into My EBSCOhost and return to your folder.
In Ebook Central, you already have an account, so you can start highlighting or taking notes as soon as you open the book. To see your notes later, just visit your bookshelf. See this link for more on Highlights, Notes and Bookmarks! Here is a link for more about the Ebook Central platform.