You can't resume a Gtk-Gnutella download with WinMX or vice-versa. Gtk-Gnutella will not overwrite existing files, it will create an alternate filename but you can't prevent it to start downloads this way. Gtk-Gnutella won't download
any file you already share (of course, the filename doesn't matter but the contents i.e., the SHA1).

You can, however, add the file to ~/.gtk-gnutella/done.sha1 or ~/.gtk-gnutella/done.namesize to prevent that it (re-)downloads the given file. You could use a simple script to add the filenames from your WinMX downloads to one of these files. Edit these files only when Gtk-Gnutella is not running, otherwise, changes to them might be lost/ignored.