You can specify the files on the command line, as tonfa writes:
$ hg commit foo.c foo.h dir/
That just works and that’s what I do all the time. You can also use the --include flag that you’ve found, and you can use it several times like this:
$ hg commit -I foo.c -I "**/*.h"
You can even use a fileset to select the files you want to commit:
$ hg commit "set:size(1k - 1MB) and not binary()"
There is no setting that will turn off the auto-add behavior and make Mercurial work like Git does. However, the mq extension might be of interest. That’s an advanced extension, but it allows you do to
$ hg qnew feature-x # create new patch
$ hg qrefresh -s foo.c # add a file to the current patch
$ hg qrefresh -s bar.c # add another file to the patch
$ hg qfinish -a # convert applied patches to normal changesets
I don’t really use MQ for this purpose myself, though, since I think it’s enough to just specify the filenames on the command line.