You will see black bars on in the preview window if they are going to be included in the encode. It's useful for setting the "cropping" of the image. (The more black bars, the larger the file size. Removing them means that Handbrake won't have to include that info in the file, and
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TV will do the right thing when displaying the file.)
Most people have this set to automatically crop the image, removing all black bars.
The image should also show you if interlacing will be an issue. If you can see horizontal lines in the image, you'll need to check the deinterlace box.
There's a complete guide on the Handbrake forum that should help you muddle through. Most people just select the Apple TV preset, check the picture for interlacing, make sure the cropping is correct, and then they start it up.
Have fun.