You can indeed only have one upload folder.
However, by importing your products via CSV, you can upload products in subfolders and then specify the subfolder in the CSV like explained above.
You could do a mix : create your products via the interface and then, upload the images manually via FTP in your subfolder.
Then, in the import screen, you could set the images via the text area:
product_code,images
my_product1,"subfolder1/image1.jpg,subfolder2/image3.jpg"
my_product2,"subfolder1/image2.jpg,subfolder2/image4.jpg"
for example.