In this article we study the MSSM with stops and Higgs scalars much lighter than gluinos and squarks of the first two generations. In this setup, one should use an effective field theory with partial supersymmetry in which the gluino and heavy squarks are integrated out in order to connect SUSY parameters (given at a high scale) to observables in the stop sector. In the construction of this effective theory, valid below the gluino mass scale, we take into account O(α3) and O(Yt,b2) effects and calculate the matching as well as the renormalization group evolution. As a result, the running of the parameters for the stop sector is modified with respect to the full MSSM and SUSY relations between parameters are broken. We show that for some couplings sizable numerical differences exist between the effective field theory approach and the naive calculation based on the MSSM running.