We construct well-known integrable equations with their Lax pairs from the corresponding linear equations using our nonlinearization scheme. Using negative powers in the spectral flow to deform the time Lax operator, we find a class of perturbations that unlike the usual perturbations, which spoil the system integrability, exhibit a twofold integrable hierarchy, including those for the KdV, modified KdV, sineGordon, nonlinear Schrödinger (NLS), and derivative NLS equations. We discover hidden possibilities of using the perturbed hierarchy of the NLS equations to amplify and control optical solitons propagating through a fiber in a doped nonlinear resonant medium.