I don't know if you can disable the amps, But if you go to manual mode, set the spider on clean red (a clean marshall sound), you can turn all effects off and should be able to use the mxr pedal. If it still sounds bad, you may want to play with the eqs from both the MXR and the amp, or you can try different amp modelings from the spider. Just make sure all distortion is off the amp model you're using because the full bore probably has the most brutal distortion on a pedal that I have heard, and may not play well with others (pardon the pun).
jbailes's post in Help Me With My Spider Iv 75w was marked as the answer