Clang tools need their builtin headers and search for them the same way Clang does. Thus, the default location to look for builtin headers is in a path $(dirname /path/to/tool)/../lib/clang/3.3/include relative to the tool binary. This works out-of-the-box for tools running from llvm’s toplevel binary directory after building clang-headers, or if the tool is running from the binary directory of a clang install next to the clang binary.
Tips: if your tool fails to find stddef.h or similar headers, call the tool with -v and look at the search paths it looks through.