In this work the authors study the multiphase flow soft-sensing problem based on a previously established framework. There are three functional modules in this framework, namely, a transient well flow model that describes the response of certain physical variables in a well, for instance, temperature, velocity and pressure, to the flow rates entering and leaving the well zones; a Markov jump process that is designed to capture the potential abrupt changes in the flow rates; and an estimation method that is adopted to estimate the underlying flow rates based on the measurements from the physical sensors installed in the well. In the previous studies, the variances of the flow rates in the Markov jump process are chosen manually. To fill this gap, in the current work two automatic approaches are proposed in order to optimize the variance estimation. Through a numerical example, we show that, when the estimation framework is used in conjunction with these two proposed variance-estimation approaches, it can achieve reasonable performance in terms of matching both the measurements of the physical sensors and the true underlying flow rates.