Each of the words in a word list has an associated score. You can change the score of individual words by viewing and editing words directly, or change all the scores in a list by selecting Change scores... from the Word List Manager's Word List menu.
To change the scores in a word list, open the Word List Manager and select the word list whose scores you want to change. Then select Change scores from the Word List menu. You can either change all the scores to a certain value, or change all the scores by a certain amount (which is usually what you want as it preserves the score ordering), or change scores of a certain value to another value.
Scores of words used in a puzzle can be adjusted (e.g. to reduce the score so that they are not reused often in subsequent fills), using Change scores of words in puzzle. Scores of each word in multiple lists can be viewed and adjusted using View/Edit words and scores on the Words menu.
During grid filling, scores can be edited in the Words Used list (button on toolbar) when you have a complete fill, or by right-clicking on a word during Manual word selection or using AutoFind.