Although Glacier has a flat structure with no hierarchy, Freeze supports the concept of folders. Folders are represented as 1 byte-sized archives with a leading slash. You can enable and disable folder view within the app by selecting "Inventory -> Folder View".
To back up a local folder to Glacier, simply drag&drop it from Finder to the target vault or the target folder within the inventory. Freeze will always inform you what's about to happen before the upload begins.
This also works if the target folder already exists at the destination. In that case, Freeze automatically determines which files need to be uploaded and allows you to synchronize the target folder with the source.
If the target folder contains archives that do not exist in the source folder, Freeze allows you to delete those "orphaned archives". If you leave "Delete orphaned archives" unchecked, Freeze will not delete any archives from the destination.