What may I refer to to learn where to locate verses or sections in the Tanach by topic? Preferably one of our own sources rather than a Christian one because the interpretations of the Tanach need to be Jewish.
To strictly answer your question, "What may I refer to," IMHO you may and you should refer to the numbers that have already become common. Many tzadikim and gedolim have already used these, including Sifrei Breslev, and there is no contradiction against the Torah in doing so. To institute or use a different numbering would only cause confusion, and detract from Torah study, and inhibit the miswah of "Ohr l'goyyim" etc.