if I use CounJoin on blockchain.info, where I have one input and one output
If you only have one input, you're not joining any coins. The point is mixing unspent outputs from several people/addresses so external observers can't figure out where each output has gone.
I understand, but if we have 3 people, I put in 5BTC, someone else puts in 2BTC, and the third person puts in 3.5BTC, the coins all get broken up into random amounts and go through two stage mix, in the end, we still have 5BTC, 2BTC, and 3.5BTC, just in new addresses. Isn't that fairly easy to track? I know I'm missing something... What is it?