iTunes reads the cover image (recommended size 1400x1400px) from the RSS feed. This image is specified (in the XML containing the podcast feed) by the tag <itunes:image href="hereGoesTheURL" />
On the other hand, Facebook reads the image (recommended size 300x300px) specified through the open graph tag <meta property="og:image" content="hereGoesTheURL" />
which has to be placed in the head section of the html code of the page containing your episode (i.e. the page that you post on Facebook).
Therefore, in principle, if you specify the iTunes cover in the RSS feed and the open graph image in the code of your website, the two images can be different and won't interfere with each other.