While there's not a specific way to save templates built into Haiku Deck currently, you can duplicate decks, which opens up the possibilities for setting up templates. This feature is currently not available on the iPhone, but we're working on it!
If you create a new deck and put it together so that it represents what you would like your template to consist of, you can keep that deck as a template and duplicate it to start a new deck using that template. Similarly, if you have an existing deck that follows the style you'd like your template to use, you can duplicate that deck and then edit the copy to make a template that can be duplicated for future projects.
On the iPad:
In the Main Menu, duplicate your deck. When you tap "Yes" in the copy prompt, a copy will be made that you can edit and customize without affecting the original. The original version will stay in the Main Menu for you to duplicate whenever you'd like.
On the web:
In your My Decks Gallery, hover over the thumbnail of the deck you'd like to duplicate. Click the little gear icon in the top right corner of the deck preview, and your slides will automatically save as a new deck. The original will stay in My Decks on haikudeck.com for you to duplicate whenever you'd like.