You can edit your video files in the Media section of your account. Click the ... button to the right of your file, and then hit edit. You will see your video in the player under the About tab, and it will let you set or reset in and out points in this window.
Keep in mind that these in and out points will only work in places where you are using Stream Monkey's player (your website) and will not apply in places where you are using the m3u8 (Apple TV, Roku or Fire TV), or sending the video (YouTube, Vimeo).
If you want the in out points to apply in all places, you'll need to set in and out points when you originally save or upload the video to your account.