I didn't even learn about metadata and cover browsing until a year after I got the reader
Here is what I do:
1) Download the book, either from here or from the store I purchase it
2) Get it into acceptable format if not already e.g. liberate it
3) Load it into Calibre. I do not keep the original after that
4) Add the appropriate tags so they appear in my collections on the reader
5) Load to the reader
My process for secure eReader is quite laborious because the HTML never seems to come out right. So I open it in a web browser, copy it into Neo Office, resave it as HTML (this adds the line breaks between paragraphs). Then I open that in my web browser, copy it and paste it back into the file using Komposer (office suites generate terrible HTML and this step removes any bad code). Then I open it one more time in Text Wrangler and do a find/replace to remove extra line breaks. The end result is a nice, clean (albeit plain) HTML file.