What is the Kodansha book? I only know the Kodansha as publishing company. But there are thousands of books. Do you mean the the Kodansha Kanji Learner’s Course?
If you are practicing Kanji next to WK it could muck up the SRS. But that depends on when you study and how well Wks SRS Intervalls work for you.
See the section: Is studying outside of WaniKani detrimental to the SRS learning process?
I think that is a thing you have to see for yourself. I don’t think anyone but you can answer that question. But both resources should teach more or less the same readings and meanings. And you can always add meanings for Kanji in WK so I don’t see how it could be confusing.