You want to open up the sound panel (either double click on the yellow speaker in the taskbar, or run sndvol32.exe (IIRC)), and Mute the microphone, then go to Options->Properties, and select "recording" and hit okay, then make sure that the microphone is the one "selected".
If you have the microphone input unmuted, when you come to playing, you'll hear both the Jesusonic output, as well as the unmodified input over each other when you play, with the above settings, the guitar goes only into Jesusonic, and the sound you hear is only that that comes out of Jesusonic.
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