In order to work on a temporary subproject, call any of the entry point functions (see Entry Points) with a simple prefix argument (<C-u>). Patcher will then prompt you for an optional subdirectory and for a specific set of files to work on, under that particular subdirectory. There, you can in fact specify files as well as directories, use wildcards, just as you would construct a shell command line diff.
Note that since the files you provide can in fact be directories, you can circumvent the Mercurial limitation mentioned above by not providing a specific subdirectory, but instead give it as a file at the second prompt. This workaround also applies to permanent subprojects, as described in the next section.