VS2005からだと思うが、stdafx.hのpragmaで指定するようになった。

こういうやつ

#if defined _M_IX86
#pragma comment(linker, "/manifestdependency:\"type='win32' name='Microsoft.Windows.Common-Controls' version='6.0.0.0' processorArchitecture='x86' publicKeyToken='31BF3856AD364E35' language='*'\"")
#elif defined _M_IA64
#pragma comment(linker, "/manifestdependency:\"type='win32' name='Microsoft.Windows.Common-Controls' version='6.0.0.0' processorArchitecture='ia64' publicKeyToken='31BF3856AD364E35' language='*'\"")
#elif defined _M_X64
#pragma comment(linker, "/manifestdependency:\"type='win32' name='Microsoft.Windows.Common-Controls' version='6.0.0.0' processorArchitecture='amd64' publicKeyToken=publicKeyToken='31BF3856AD364E35'language='*'\"")
#else
#pragma comment(linker, "/manifestdependency:\"type='win32' name='Microsoft.Windows.Common-Controls' version='6.0.0.0' processorArchitecture='*' publicKeyToken='31BF3856AD364E35' language='*'\"")
#endif


とりあえず空でWTLプロジェクト作ってstdafx.hの該当行コピれ。