The procedure to calculate masses and matrix-elements in the presence of mixing of the basis states is explained in detail. We then apply this procedure to the two-loop calculation in Chiral Perturbation Theory of pseudoscalar masses and decay constants including quark mass isospin breaking. These results are used to update our analysis of $K_{\ell4}$ done previously and obtain a value of $m_u/m_d$ in addition to values for the low-energy-constants $L_i^r$.