First Off, What the Heck Is a Query?
Glad you asked! A query is part of a URL containing a question mark and information about the page in question. Here's a URL that contains a query: http://www.yoursite.com/download.php?product=14. See that "product=14" bit that comes right after the question mark? That's the query. Queries appear in the URLs of files written in a scripting language such as PHP or ASP.
How Do I Keep Sitemapper From Mapping URLs With Queries?
By default, Sitemapper follows URLS with queries. To ignore any specific queries, click the Settings button in the Toolbar and go to URLs and Queries to Ignore. Enter the query you wish to ignore in the field on the right, and then click the Add button. This adds the query to the list on the left. When you're done specifying the queries you want to ignore, click OK.
Now when you scan your site, all the URLs containing the query or queries you specified will be ignored.
Why Would I Want to Ignore Queries?
The same reason you might want to ignore any given page on your Website. The only reason the URLs and Queries to Ignore tool is separate from the URLs and Queries to Ignore is because scripting languages work differently than the other files you may wish to ignore.