@Turran: The upper resolution display in the main window shows the number of pixels per line and the number of lines at all the Indi will output. These are the picture dimensions your screen will receive. They are also shown in the VGA modes window where they can be altered. It's a good thing to start here with your monitor's native resolution or at least with a VGA mode that corresponds to your monitors aspect ratio.
The lower resolution display shows the actual picture size. Try values equal to the upper ones and see what happens. You may or may not use doubled lines here. If the picture fits almost perfect you might fine-tune the position with H- and V-offsets.
Still, I can't figure out which frequency values are optimal for my screen settings. Documentation is strongly required.