Since you never made an intro post, I never linked you to any of the threads I usually do:
Guide for using Anki 2 with TextFugu:
http://www.textfugu.com/bb/topic/guide-to-using-anki-2-with-textfugu/
Track your progress and share your ideas/concerns when you finish a season (gain a level ^_^):
http://www.textfugu.com/bb/topic/textfugu-season-completions-for-great-motivation-of-heart
List of additional Japanese resources you may find helpful:
http://www.textfugu.com/bb/topic/japanese-learning-resources/
List of Common Errors in TextFugu:
http://www.textfugu.com/bb/topic/common-errors-in-textfugu/
As far as I’m aware, the hiragana doesn’t get replaced with Kanji later on as that would advance it way past beginners level, which is the goal of TextFugu. Yes you should be using the Radical/Kanji/Kanji Vocab decks linked into the seasons, as they will teach vocab using Kanji rather than just Hiragana. The point of this is to approach Kanji in a systematic way without limiting the vocab he can teach due to complicated Kanji.
If you wish to add new cards to the deck or modify the existing card to use the Kanji instead, it won’t break anything.