A system for modulating neural tissue in a patient comprising: an implantable neural stimulator comprising one or more electrodes (254, 238), at least one antenna and an electrode interface (112, 252); a radio-frequency pulse generator module comprising an antenna module configured to send one or more input signals to the at least one antenna of the implantable neural stimulator through electrical radiative coupling, the input signal containing electrical energy and polarity assignment information that designates polarity assignments of one or more electrodes (254, 238) in the implantable neural stimulator, wherein the antenna module is further configured to transmit to the implantable neural stimulator a first input signal containing the electrical energy and a second input signal containing the polarity assignment information, wherein the first input signal has a different carrier frequency than the second input signal; and wherein the implantable neural stimulator is configured to: control the electrode interface (112, 252) such that the one or more electrodes (254, 238) have the polarity assignments designated by the polarity assignment information, create one or more electrical pulses suitable for modulation of neural tissue using the electrical energy contained in the input signal, and supply the one or more electrical pulses to the one or more electrodes (254, 238) through the electrode interface (112, 252) such that the one or more electrodes (254, 238) apply the electrical pulses to the neural tissue with the polarity assignments designated by the polarity assignment information. an implantable neural stimulator comprising one or more electrodes (254, 238), at least one antenna and an electrode interface (112, 252); a radio-frequency pulse generator module comprising an antenna module configured to send one or more input signals to the at least one antenna of the implantable neural stimulator through electrical radiative coupling, the input signal containing electrical energy and polarity assignment information that designates polarity assignments of one or more electrodes (254, 238) in the implantable neural stimulator, wherein the antenna module is further configured to transmit to the implantable neural stimulator a first input signal containing the electrical energy and a second input signal containing the polarity assignment information, wherein the first input signal has a different carrier frequency than the second input signal; and wherein the implantable neural stimulator is configured to: control the electrode interface (112, 252) such that the one or more electrodes (254, 238) have the polarity assignments designated by the polarity assignment information, create one or more electrical pulses suitable for modulation of neural tissue using the electrical energy contained in the input signal, and supply the one or more electrical pulses to the one or more electrodes (254, 238) through the electrode interface (112, 252) such that the one or more electrodes (254, 238) apply the electrical pulses to the neural tissue with the polarity assignments designated by the polarity assignment information. control the electrode interface (112, 252) such that the one or more electrodes (254, 238) have the polarity assignments designated by the polarity assignment information, create one or more electrical pulses suitable for modulation of neural tissue using the electrical energy contained in the input signal, and supply the one or more electrical pulses to the one or more electrodes (254, 238) through the electrode interface (112, 252) such that the one or more electrodes (254, 238) apply the electrical pulses to the neural tissue with the polarity assignments designated by the polarity assignment information.