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This is the second in a series of papers which intend to explore conceptual ways of distinguishing between families in the $q$-Askey scheme and uniform ways of parametrizing the families. For a system of polynomials $p_n(x)$ in the $q$-Askey scheme satisfying $Lp_n=h_np_n$ with $L$ a second order $q$-difference operator the $q$-Zhedanov algebra is the algebra generated by operators $L$ and $X$ (multiplication by $x$). It has two relations in which essentially five coefficients occur. Vanishing of one or more of the coefficients corresponds to a subfamily or limit family of the Askey-Wilson polynomials. An arrow from one family to another means that in the latter family one more coefficient vanishes. This yields the $q$-Zhedanov scheme given in this paper. The $q$-hypergeometric expression of $p_n(x)$ can be interpreted as an expansion of $p_n(x)$ in terms of certain Newton polynomials. In our previous paper arXiv:2108.03858 we used Verde-Star's clean parametrization of such expansions and we obtained a $q$-Verde-Star scheme, where vanishing of one or more of these parameters corresponds to a subfamily or limit family. The actions of the operators $L$ and $X$ on the Newton polynomials can be expressed in terms of the Verde-Star parameters, and thus the coefficients for the $q$-Zhedanov algebra can be expressed in terms of these parameters. There are interesting differences between the $q$-Verde-Star scheme and the $q$-Zhedanov scheme, which are discussed in the paper.