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We present a new modeling method for cladding-pumped highly Er-Yb co-doped fiber amplifiers. The method combines the beam propagation method (BPM) for the field propagation and nonlinear rate equations for the laser medium. The pump absorption, which is obtained numerically from the nonlinear rate equations, is used in BPM calculations of the field propagation. As a result, our method can effectively deal with difficult issues such as the multimode nature of cladding pumped schemes even in complicated structures, as well as strong nonlinearities in highly Er-Yb-doped fiber amplifiers. The simulation results are in very good agreement with experiments having different structures and different concentrations of Er-Yb. The method is particularly well suited to active fibers with low amplified spontaneous emission power, but it can also be developed further for more general cases.