A pressure support system comprising: a pressure generator configured to generate a pressurized flow of breathable gas for delivery to the airway of a subject; a processor configured to execute computer program modules, the computer program modules comprising: a first mode module configured to control the pressure generator in accordance with a first mode of therapy wherein breathing cues are provided to the subject in accordance with a breathing regime using the pressurized flow of breathable gas, wherein the breathing cues prompt the subject to consciously alter one or more breathing parameters of respiration; and a second mode module configured to control the pressure generator in accordance with a second mode of therapy wherein the flow of breathable gas is provided to the airway of the subject at a selected pressure or selectively variable pressures; a transition module configured to transition between the first mode of therapy and a second mode of therapy wherein a pressure level of the gas in the pressurized flow of breathable gas is adjusted in response to a trigger event characterized in that the transition provided by the transition module between the first mode of therapy and the second mode of therapy includes a gradual adjustment of the pressure level of the gas in the pressurized flow of breathable gas. a pressure generator configured to generate a pressurized flow of breathable gas for delivery to the airway of a subject; a processor configured to execute computer program modules, the computer program modules comprising: a first mode module configured to control the pressure generator in accordance with a first mode of therapy wherein breathing cues are provided to the subject in accordance with a breathing regime using the pressurized flow of breathable gas, wherein the breathing cues prompt the subject to consciously alter one or more breathing parameters of respiration; and a second mode module configured to control the pressure generator in accordance with a second mode of therapy wherein the flow of breathable gas is provided to the airway of the subject at a selected pressure or selectively variable pressures; a transition module configured to transition between the first mode of therapy and a second mode of therapy wherein a pressure level of the gas in the pressurized flow of breathable gas is adjusted in response to a trigger event characterized in that the transition provided by the transition module between the first mode of therapy and the second mode of therapy includes a gradual adjustment of the pressure level of the gas in the pressurized flow of breathable gas. a first mode module configured to control the pressure generator in accordance with a first mode of therapy wherein breathing cues are provided to the subject in accordance with a breathing regime using the pressurized flow of breathable gas, wherein the breathing cues prompt the subject to consciously alter one or more breathing parameters of respiration; and a second mode module configured to control the pressure generator in accordance with a second mode of therapy wherein the flow of breathable gas is provided to the airway of the subject at a selected pressure or selectively variable pressures; a transition module configured to transition between the first mode of therapy and a second mode of therapy wherein a pressure level of the gas in the pressurized flow of breathable gas is adjusted in response to a trigger event characterized in that the transition provided by the transition module between the first mode of therapy and the second mode of therapy includes a gradual adjustment of the pressure level of the gas in the pressurized flow of breathable gas.