When doing one of the species exercises from the "exercises" menu the style rules will all be preset according to the species being studied. This doesn't stop you from doing species exercises with modified style rules, though - you can always set up a practice window to use whatever style you prefer. The difference is that if you are doing this for a class, your "score" on the exercise will reflect your understanding of the rules built into the exercises.
The default window in Counterpointer is the free practice window - here you can write anything you please, or open a file composed earlier, and evaluate it according to whatever style rules interest you.
To choose the style, press the Style button above the screen piano. A window will appear with multiple choices regarding style.
Certain of the style rules have been assembled into sets: if you choose "Palestrina," for example, Counterpointer will select rules in each category that would be appropriate in the Palestrina style. Similarly, you can choose to work with the vocal style of J.S. Bach. There are also buttons for each of the Species styles well known from traditional counterpoint studies.
You can modify any style set as you like, and if you wish you can save your custom style for later use.
For example, you might want to start with the Palestrina style and make a few alterations. Once you've made your choices in each of the style categories (rhythm, independence of voices, dissonance handling, etc.) press the Save Style button and give your custom style a name. The file should have the extension .csf (Counterpointer Style File) for compatibility with the Windows version of Counterpointer.
There are different schools of thought concerning the rules appropriate to each species. If you find that your own study would benefit from changes to the species styles supplied with Counterpointer, you can make your own modified species rules.
Make the changes as needed and save your file under an appropriate name, e.g. "MyFirstSpecies.csf." Then use the Generate C.F. command to create a random cantus firmus, or write a cantus firmus in one of the staves. You can evaluate the exercise using your customized style rules.
If doing free counterpoint exercises or practicing with custom styles you may find it convenient to set up a template for the type of score you'll be using. For example, you could set up a score with three staves using your choice of clefs and instruments. If you then use the "Save as Default Layout" command in the File menu, Counterpointer will use that layout whenever you click the "New" button to begin a fresh file.