Using Sigil's metadata editor I added a second title metadata element and added to it the attribute subtitle. When I ran the Generate Cover plugin it used the subtitle. Back in Sigil's metadata editor I used the arrows to move the subtitle below the main title and that fixed it.
Code:
<dc:title>Fishpingle</dc:title>
<dc:title id="tle">A romance of the countryside</dc:title>
<meta refines="#tle" property="title-type">subtitle</meta>