There is an option in the uploader to save a copy of transmitted photos to a folder.
I have this setup for each client/server connection I have saved so I can easily check what has been sent if I accidentally close the contact sheet and lose the green squares.
I have that too but it's not the same. Having to manually match up file names to determine what has been uploaded is time consuming.
A visual indicator, or at least a filterable tag, would negate the need for a sent folder.
So, there's a few things to address here, but I think the thing to address first is the visual indicator. The little green square that shows as you upload the file should remain there while the Contact Sheet is open. The only way I know of to make this disappear while the Contact Sheet remains open is to go to Finder or Windows explorer (or some other application) and rename the file itself. If you can provide more details about what circumstances cause the indicator to disappear for you, that would be helpful. If you aren't sure, I would be happy to screenshare with you to determine if there is a bug or something that you can avoid doing to make this indicator persist.
And then to tack on to what Kevin said, there is an option in the "edit" menu that I wanted to make sure you are aware of: you can choose "Select Transferred" to select any items on the contact sheet that have been successfully uploaded. From there you can use color labels, tags, star ratings or the metadata template to add any kind of information you want to the uploaded images. There's still a few steps to make that happen but I'd say its much simpler than matching up the originals files with what ends up in a folder of copies of the uploaded files. Would this suit your needs?
Doing this automatically has a number of complications. Kirk details a few of them here, and while it is quite an old thread, it is still relevant:
https://forums.camerabits.com/index.php?topic=3779.msg17000#msg17000