The Preference menu will appear in different place depending on the Operating System and version you are using. You can check the Help Menu, Edit Menu, Apple Menu or the Finder Menu. There are;

Printing Preferences which control Puzzle, Border, Footer, Across/Down headings and Answer Hint Options.

Crossword Colours Preferences which allows you to select your colours or turn on Black and White printing.

Layout allows you to select a full range of options eg number of clue columns, type of solution (small or large), first word location, Fonts, Font sizes and whether to scale the puzzle to fit the puzzle area. What this does is if you reduce the puzzle to 15x15 it will scale it to fill the 25x20 crossword area.

Misc. only one option here at the moment which controls the password you want saved with the puzzle. This is necessary for the Crossword Wizard Player so that teachers can reveal to students the answer to the puzzle.

Clicking the Make Default button will save these options as defaults for the program to use the next time it runs.