If you release a cover song as a single and later want to include it in an album, that's totally fine—but you'll need to purchase a separate cover license for each instance.
Each time a cover song is uploaded to eMastered, whether as a standalone or as part of another release, you must check the "Cover Song" box and pay for a new license.
This ensures the original songwriter receives the required royalties for every upload. There's no option to purchase one blanket license for multiple uses like a full album or discography—each cover song in each release requires its own individual license.
For more info on how to add your release as a cover check out this article.