Chris (Muse Bassist) uses clean bass from amp 1, Microsynth (square wave setting) and a bit of fuzz. then just mixed together in amp 2. recording it, Take the clean Amp mic ch 1, DI into the FX into Ch 2 the FX can have the bottom rolled off to stop it altering the clean bass, The fx is blended in to the clean until you have the right sound..