Freezing soup, then transferring it to bags
Many suggestions for you:


line the containers with the bags, folding the edges down over the container. Pour the soup into the supported bag. When it's frozen it should be easy to remove and you have the container back.
buy plastic (for flexibility) containers, 6 or 8 of them. Freeze in these instead of bags. It's easier to pop the frozen soup out of them, and you don't mind if they are "occupied" in the freezer until the soup is eaten.
as above but you pop them out frozen into a large freezer bag. I do this with large-batch soups like pumpkin or borscht and don't need to wrap each soup block within the larger bag
use something completely different, such as a bowl that you might eat of, to support the bag while you're pouring the soup in. Seal the bag, take it out of the bowl, and lay it on its side to freeze. Later, stand them up in the freezer for easier sorting


Pretty much anything would be better than rigid glass containers that you don't want to leave in the freezer.