From Brent Kelley,
Your Guide to Golf.
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There are examples above of two different ways to mark the scorecard when using handicaps in stroke play. The top version is the more common, at least among players with lower handicaps. (The following page has an example of a higher-handicapper's scorecard.) Remember, when we talk about taking strokes on the golf course or scorecard, we're always talking about course handicap, not handicap index. And for the true beginners reading this, "taking strokes" or "taking a stroke" means that your course handicap allows you to reduce your score by one or possibly more strokes on certain holes.

Always start by marking the holes on which you get to take a stroke. Make a little dot somewhere within the box for the holes on which your course handicap will be used. (The "handicap" row of the scorecard tells you where to take strokes. If your course handicap is 2, then take a stroke on the holes marked 1 and 2. If it's 8, then on holes designated 1 through 8. More here). If marking the card in the manner of the top example, also divide each of those boxes with a slash.

Write down your strokes taken on each hole as you normally would. The gross score (your actual strokes played) goes on top. Then, on holes where you are taking a stroke, write your net score (your actual strokes minus any handicap strokes) below the gross score.

When you tally up the total, again write your gross score on top and net score below the gross.