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I played a game today against someone who thought they did not need a handicap. However at the end of the game I had 79 pionts of territory, my opponent had some. Using Japanese counting we put the prisoners back into the territories of the same color, but black, my opponent, still had 26 prisoners left to be placed back on the board.
How do you deal with a situation like this?
Bass: You can do a kind of prisoner swap: for every prisoner that you return to your opponent's bowl, pick one of your stones off the board and place it into your bowl, so that your territory increases by one point for every prisoner returned. When every prisoner has been returned, your territory will reflect the winning margin.
The more boring way is just to count one point for every leftover prisoner and add that count to the winner's territory.
Edit: When counting an exceptionally long game it is possible that both players have leftover prisoners. In this case, an equal number of prisoners of each color can be returned to the bowls without affecting the final result. This is also useful during the game if you are running low on stones. (Happens all the time with the sets that are in public use at the local pub :-)
the game score is the difference in player points, where player points is territory minus captures
but whether you subtract your lost stones from your own territory, or add them to your opponent's ... the difference in scores will be the same.
for example: black has 20 points of territory, but white captured 50 of his stones. white has 200 points of territory, and black only captured 10
black's score is 20 - 50 = -30 (30 stones left over) white's score is 80 - 10 = 70
game score, white wins by 100 (70 minus -30)
or...
black's score can be 20 + 10 (white prisoners) = 30 white's score can be 80 + 50 (black prisoners) = 130 game score is still white wins by 100 (130 - 30)... but this method is not easy to count, because you can't just put the prisoners back on the board)
short answer (for easy counting), for every extra black prisoner, remove a white stone from the board and put them all back in the bowls (giving white that much more territory). The difference in points will still be the same score. (basicly, the same as Bass says above)
You can deal with this in another way... as soon as you're visibly (for the weaker player) ahead you can indicate, that starting another game might be more enlightening.
A friend in the local go club prefers to play me without handicap (despite currently about 6 stones difference in strength), but resigns in time. Being crushed like that (as long as you can cope with the experience) teaches you a different set of skills than the ordinary handicap game. It exposes many of your weak, overambitious plays as what they are, helping much in playing more solidly in future.
The custom when I was learning go was to hand the opponent the extra stones and say, "Here is your change." :)
as you know: one space of territory = 1 point
to answer your question: each stone that a player captures gives them 1 point, their captured pieces are then used to cancel out points for both sides. In your case, your opponent has as many points as he has territory left + however many captured stones he has left.