What exactly do you mean by "manifest embedded theming"? OpenMPT has a manifest that allows custom XP (Vista?) themes.
Correct there's one in the resource file (also with ID 1 which is correct) but changes to VS2008+ this doesn't work anymore.
You'll specifically have to link this e.g. :
#pragma comment(linker,"/manifestdependency:\"type='win32' name='Microsoft.Windows.Common-Controls' version='6.0.0.0' processorArchitecture='x86' publicKeyToken='6595b64144ccf1df' language='*'\"")
Your manifest in the resource will still be working on older compilers AND newer compilers and it supports different chipsets.
I'll post the code here, you'll have to paste it in stdafx.h
#if _MSC_VER >= 1500 //compiler VS2008 or higher?
#if defined _M_IX86
#pragma comment(linker,"/manifestdependency:\"type='win32' name='Microsoft.Windows.Common-Controls' version='6.0.0.0' processorArchitecture='x86' publicKeyToken='6595b64144ccf1df' language='*'\"")
#elif defined _M_IA64
#pragma comment(linker,"/manifestdependency:\"type='win32' name='Microsoft.Windows.Common-Controls' version='6.0.0.0' processorArchitecture='ia64' publicKeyToken='6595b64144ccf1df' language='*'\"")
#elif defined _M_X64
#pragma comment(linker,"/manifestdependency:\"type='win32' name='Microsoft.Windows.Common-Controls' version='6.0.0.0' processorArchitecture='amd64' publicKeyToken='6595b64144ccf1df' language='*'\"")
#else
#pragma comment(linker,"/manifestdependency:\"type='win32' name='Microsoft.Windows.Common-Controls' version='6.0.0.0' processorArchitecture='*' publicKeyToken='6595b64144ccf1df' language='*'\"")
#endif
#endif