I'm sorry, I'm a bit confused by what you mean, exactly. The FX Mappings, of the Mixer FX window can be applied to both channels. The Channel 1 and Channel 2 strips of the Mixer FX window simply select and indicate how these are applied. Saving a preset, in the "MX"/Mixer FX panel of the Presets window, should save the FX Mappings portion of the Mixer FX. Triggering the preset should then overwrite the FX Mappings. It doesn't save or overwrite the positions of the Channel 1/Channel 2 knobs and buttons (which should reflect whatever is happening on your mixer).