Your explanation is indeed unclear. I will try to tell all the things that happen there, hoping that some of them will make it clear for you what you see and what you were asking.
When you send a transaction, if you want to pay for example 0.001
BTC, you will actually spend maybe 0.00100300
BTC(*) because you actually pay some transaction fees (the miners' work).
Also, if you have received 0.002
BTC and that's what you are spending from, the whole 0.002
BTC is "sent away", but 0.002 - 0.00100300 = 0.000997
BTC will return to you, either into a change address, either into the address you were sending from, depending on your settings.
The fee amount doesn't help in your privacy. The use of change addresses does.
(*) The numbers are not accurate, the fee depends on how busy the network is and your settings. But the numbers may make it clearer then xxx and yyy