There is no special way to notate a thumb-over. You can use the thumb-over whenever you only need to play the lowest string of a chord that is normally barred, such as the altered F major chord shown in the tab. The thumb-over can hold down the F note bass on the low E string with the thumb and use the remaining fingers to hold down the rest of the chord while letting the high E string ring open.

A thumb-over can be used in place of another finger to hold down the lowest string to give the other fingers more freedom to be placed elsewhere. A thumb-over can be used to fret the lowest 2 strings as well, but is rarely used as there is usually a more convenient way to fret those notes.

To make a thumb-over position more comfortable, move your wrist higher to give your thumb more space to do a thumb-over with. This may be less comfortable if you're pressing down on the other strings with your other fingers, so find a balance that works for you.