Hi Patty,
No, there is no such thing as a universal "good" size. Best thing to do is judge the fabric itself: does it have a repeating pattern? If so, try to capture a single repeat, or a number of repeats if that is easier.
After you make the full scan, simply click and drag to make a selection within the image that Fablib shows to choose which part you want to keep. By default, this selection will be a square, but you can change that by clicking on the "Settings..."-button and uncheck "Force square selections".
Also, when you click "Fine Tuning", Fablib will show how your selected area looks when it is repeated.
Hope this helps,
Arnout