I have been going through my 2001 Stratus SE for the last couple months replacing almost all of the suspension parts. At one point, I was advised that my drivers CV axle was going bad by a person at a shop that I thought was reputable. (turns out it was the Tie Rod end I had just replaced was the passenger side end in a driver side box.. #NotSoReputable) So I went about researching and figuring out how to replace it. About 2 months ago, I did the job and replaced the axle seal while I was at it. I measured the fluid that came out and since my differential didn't have a plug or anything, I added it where the automatic trans fluid normally goes in.
Now here is the scary part.
I have been noticing a clunk when I let off the throttle or when I get on the throttle or when I put it in gear.
I had it aligned today and the mechanic said the new axle a bad again, and that is what is making the clunk. But I cant help but have the feeling that I didn't put the fluid back in the right place after I replaced the first axle.
So here is my question: Does the transmission share fluid with the differential? If it doesnt share, where do I refill the differential when changing the CV axle?

My Chilton manual doesn't say anything about it in either the section from replacing the CV axle or the Checking the fluid section. Every Video i watch online just kinda skips the topic by saying "Put it back in" or "installation is the same as removal"... Any help is greatly appreciated..

 

..yes

 

Thank you @primem helped me out a ton. However i have another question:
Does anyone know where I can get a locking spindle nut? The axle I have isn't drilled for a cotter pin, and the only thing coming up at part stores is a castle nut, or a "knock down" style nut that you hit with a hammer to lock it in place. That just doesn't seem like something that I would want on the new axle, and I don't want to reuse the one it came with.