My flymake settings for C/C++

.dir-locals.el

;; just an example
((c++-mode . ((flymake-additional-clang-flags . ("-I../" "-std=c++0x")))))

my-cc-flymake-settings.el

(require 'flymake)

(defvar flymake-additional-clang-flags nil)
(put 'flymake-additional-clang-flags 'safe-local-variable 'listp)

;; no need to arrange Makefile
(defun flymake-cc-init ()
  `("clang"
    ("-fsyntax-only" "-Weverything"
     ,@flymake-additional-clang-flags
     ,(file-name-nondirectory
       (flymake-proc-init-create-temp-buffer-copy
        'flymake-create-temp-inplace)))))

;; (push (list (rx "." (or "c" "h" "cc" "cpp" "hh") eos)
;;       #'flymake-cc-init)
;;       flymake-proc-allowed-file-name-masks)

;; (add-hook 'c-mode-hook #'flymake-mode)
;; (add-hook 'c++-mode-hook #'flymake-mode)

With a recent enough version of Flymake, all you have to do is to set flymake-cc-command like

(setq flymake-cc-command `("clang" "-fsyntax-only" "-Weverything" "-x" "c" "-"))