Kobo covers 101: The cover images are generated from fhe first page of the book. If that looks good, then the cover should look good.
From the sounds of it, the covers you want are on the first page, but are not centred and automatically sized to fill the page. You can fix that manually by editing the book and changing the code in the page. But, using either the Polish Books function of calibre, or the Modify ePub plugin should do this as well. Both of these update the files in the library, and will skip the save to disk and re-add that you are doing.
An alternative is what the other David suggested. The driver can send the cover files to the device when the book is sent. The options David was pointing to will do this. If the book is already on the device and you don't want to change it, you can use the Kobo Utilities plugin to send the covers separately.
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