Changing artwork in iFlicks can be done in multiple ways. The easiest is to choose a suitable cover from the artwork selector if the default artwork is not what you are looking for.
If you have your own artwork which you would like to use, you can drag it directly onto the currently used cover in the metadata sidebar.
It is also possible to use rules to change the artwork. This can be used if you want to use one specific cover for all episodes of a TV Show season or series for example.