Open your downloaded template file in your favorite Japanese-capable text editor. Edit the file so that it has the right number of Kanji for each lesson, and make any other graphical or layout changes you like. Then replace all the X's with your Kanji characters.
Finally, you'll have to edit the URL's for each Kanji so that the links from each character go to the right file on the Project site. The Kanji data pages are all identified by a unique, 4-digit number called the kuten code. To help you look up the kuten code for your Kanji, we have created this kuten page.
On the kuten page, look up each of your characters (they're listed alphabetically by on-yomi), and click on it to see its information. Change the KKKK in each spot in your Kanji page to the appropriate number, and repeat until all your Kanji are complete.