Hey, Sound:
Your problem probably lies in the fact that you are direct inputing a pedal that is designed to work with an amplifier. Here's a excerpt from the ME-50 overview:
"Designed to work with your amplifier, the ME-50 focuses on killer multi-effects (like COSM® overdrive and distortion) rather than amp modeling."
It's an effects modeler, not an amp modeler (i.e., not a POD). So, if you are going from the guitar outs to your computer interface, it will likely sound pretty bad -- just like using a direct line from a typical stomp box.
The unit's manual says it has a headphone out, which can be fitted with a Y chord to go into a mixer. If you must go direct, that is probably a preferable route. However, based on its description, I'd guess that the unit would probably produce the best sounds through an amp into a microphone.
Good luck!
- Kevin