I place my zip files into the folder I want them to stay in. Then once I unzip, I move the zip file.
I sort my files by Site and then by Designer. It takes time to set it up, but once you are done, it is much easier to find what you are looking for is you know which site & designer. Since I use 99% GDS, that makes the first step easier for me.
Good luck, I am sure others will give you much better advice than I have.