You move the red box initially to cover the area of the screen that the content will be scrolling through -- so usually it will cover the entire size of the window on the screen; you will be able to trim off scrollbars and stuff later so don't even worry about that. The fact that you almost always want to capture the entire window contents is why normally you leave the red box to autosize to the window.
Then you follow the instructions and scroll the contents of the window with the mouse or keys, and hit prtscr after each scroll.
Did you watch the video here:
https://www.donation...c/3ds/sc29/sc29.htmlIn the end Screenshot Captor will stitch all the images together and let you tweak how they are stitched.