I use Gimp for that. in addition to what has been said (import both images as layers, flip one, resize/rotate to get both sides aligned, adjust transparency of the upper one) i like to alter the color in order to distinguish better what is on which side. A proper "levels" balance helps a lot in distingushing details.
Then highlighting the traces on nex layers can help in knowing what is traced and what is not. I use the pencil, with [Shift] to make straight lines, and [Ctrl] to make them horizontal, vertical or 45°.
A couple of examples :
To guesstimate the tracks under components, think of the shortest path the track will take. And don't forget vias !
An application schematic for the device helps a lot too.