The only difference between the throwout bearing noise and the pilot bearing noise (inside flywheel) would be how far you have to push the pedal to stop the noise. If you only have to push the clutch slightly to half way down to stop it, its the throw out bearing. If you have to push the clutch pedal to the floor to stop the noise its the pilot bearing.
Either way when you do the clutch you should replace all of these bearings anyway.

 

So is there an input shaft bearing that could be bad? How does the mechanic come up with it. I have to push the pedal all the way down for it to stop. So this would be theclutch? Or is there anyway it could be the trans? Trans shifts great with no problems thats why I have a problem with the tranny being the problem lol