When uploading media elements the first item uploaded will be marked at the thumbnail, as indicated by a small star icon. You may change the thumbnail by clicking the gear icon below the desired thumbnail image, and select Use as Thumbnail.
Depending upon the current active template, the thumbnail will be displayed at a number of possible bounding constraints. Click the gear icon below the current thumbnail and select "Edit Thumbnail" to load the thumbnail edit view. This page includes the size constraints for thumbnails used by the active theme, tools for making for a custom image crop, and the option to upload a new thumbnail.
By default, Dunked will automatically crop the thumbnail to meet the needs of the active template. Using the custom crop tool, will give you better fine grain control of the actual crop. When cropping, be sure that the crop size (displayed in the upper right corner) is larger than the template thumbnail size (displayed in the upper left corner).