Don't have your CAPS LOCK on when entering numbers. Then entered numbers are tiny (about 1/16 normal size) and locate in the upper-left corner of the square. You don't have to restart the game to change it, just toggle off the CAPS LOCK and overtype the small numbers.
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Shift and the number (or CAPS-LOCK) is for entering possible numbers (as mentioned on the product page). That way you can keep track of the possible solutions.
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