The microwave properties of polycrystalline MgB2 thin films prepared by the so-called in-situ method are investigated. The characterization of the films at microwave frequencies was obtained by a coplanar resonator technique. The analysis of the experimental data results in the determination of penetration depth, surface impedance and complex conductivity. The aim of this work is to set the experimental results in a consistent framework, involving the two-band model in the presence of impurity scattering. The energy gaps are calculated and the contribution of intra- and inter-band scattering is considered. From the comparison between the calculated gap values and the experimental data it turns out that the temperature dependence of the penetration depth can be accounted for by an effective mean energy gap, in agreement with the predictions of Kogan et al. [Phys. Rev. B 69, 132506 (2004)]. On the other hand, the temperature dependence of the real part of the microwave conductivity and of the surface resistance is accounted for by the single smaller gap, in agreement with the work of Jin et al. [Phys. Rev. Lett. 91, 127006 (2003)]. Since these findings rely on the same calculated gap structure, the required consistency is fulfilled.