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Downloading a cover only adds it to calibre's library. It doesn't actually change anything in the epub itself.
There are several ways you can insert the new cover into the epub itself.
1. Reconvert the epub (If the original book is epub, you can still run an epub to epub conversion).
2. Edit the book with Sigil. The Open With plugin is useful if you want to use this method.
3. Use the Modify Epub plugin to insert the cover without reconverting.
#1 is the easiest because it doesn't require additional plugins. However, it may have some unintended consequences because you're doing a full conversion on the book. #3 requires you to install a plugin, but after that it's just as easy as #1, and avoids the issues that may arise with a full conversion.
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