Once your iPad is connected to an output device (e.g. projector, flat panel monitor etc.), what you see in the preview area of TrialPad will exactly match the aspect ratio of the output device. For example, if you have a television that has a widescreen 16:9 aspect ratio, it has to be displayed inside TrialPad's preview screen, which is a more square shape. The result is that a widescreen can only fit into a square with gray bars at the top and bottom to fill the unused space.
You may have seen a similar issue when an older television show with a 4:3 aspect ratio is displayed on a new widescreen television, the result in that situation is gray bars on the sides. To fill the screen the image would have to be stretched, and therefore distorted, and we don't want to do this in TrialPad. See http://en.wikipedia.org/wiki/Display_resolution
You will get a better user experience if you choose a 1024x768 resolution on the projector (4:3 aspect ratio), and choose that same resolution in the Settings within TrialPad. However, if you are using an Apple TV it will be widescreen and you will not have the option to adjust the output resolution.
Devices which output to the Apple TV via AirPlay have no control over the resolution that is negotiated between the Apple TV and the output device, and the resolution shown in TrialPad’s settings is the resolution of the content being sent from your iPad to the Apple TV. Your iPad can only control the resolution if it is the device that is directly connected to the output device.
To deal with this issue TrialPad allows you to collapse/hide the document list to have a larger preview area by pressing the Expand button at the top left corner of the preview screen (it looks like a two-headed arrow). Hiding and showing the document list during a presentation does not affect what the audience sees.