Hey I bought a used 2000 E46 328i with a lil under 100k miles on it.
Whenever I shift, I hear a kind of clunking noise in the back. I can hear the gears being changed in the transmission.
I dont mean when i press the clutch, or release it to get it INTO gear. I mean even when im holding the clutch down and I shift thru the gears with the engine not running I can hear the sound coming from the back. Is this normal? If not, what can possibly be the problem? TYI

Most likely its your diff. bushings. If you can lift the rear end up and get a prybar on them that would be the first thing i would check.

you might also want to check the transmission bolts, make sure their torked down properly.

"I mean even when im holding the clutch down and I shift thru the gears with the engine not running I can hear the sound coming from the back. Is this normal? If not, what can possibly be the problem? TYI"

It's not clear to me how any torque could be transmitted to the rear end without the engine running. You might have a second person listen and help locate the sound. With the engine running, the sound could be any of the above including a bad u-joint.