If there are two or more system administrators who wish to maintain software separately, or if there is any other reason to want two or more stow directories, it can be done by creating a file named .stow in each stow directory. The presence of /usr/local/foo/.stow informs Stow that, though foo is not the current stow directory, even if it is a subdirectory of the target directory, nevertheless it is a stow directory and as such Stow doesn’t “own” anything in it (see Installing Packages). This will protect the contents of foo from a ‘stow -D’, for instance.
When multiple stow directories share a target tree, if a tree-folding symlink is encountered and needs to be split open during an installation, as long as the top-level stow directory into which the existing symlink points contains .stow, Stow knows how to split open the tree in the correct manner.