I tried to upload an entire folder to GDocs using Upload->Folder, but it did not behave the way I wanted. So I wrote a small program that tells me which folders contain any files, and then I upload each of those folders using Upload->Files. The program looks like this:
I can switch between the accounts sunamoAdventist and sunamoCZ. For each account, it lists the folders that contain some files. I press delete on the folder I have just uploaded and the folder disappears so it does not get in the way. It is primitive but very practical :).