Go to your Theme Options then the Layout & Settings tab. The last option is “Slideshow behavior on overview pages”. Select the last option in that dropdown for “Display only single image on overview pages and all slideshow images except the first one on single entries”.
This will make it so your thumbnails act as previews to the content but don’t show up on the single portfolio page/single blog page or in their slideshows. You could also select the option just before this one so that the thumbnail is also included in the slideshow if you would like.