For 32-bits application:
On 64-bit platforms, it runs on WOW64 and accesses 32-bit registry (inside Wow6432Node).
For 64-bits application:
On 64-bit platforms, it runs natively and accesses 64-bit registry (not inside Wow6432Node).
Whatever, you can explicitly indicate which version of registry you want to access, just use RegOpenKeyEx function with KEY_WOW64_32KEY or KEY_WOW64_64KEY in the desired access rights parameter.
Example: A 32-bit application running on WOW64 accesses the 64-bit registry
HKEY hkResult = NULL;
REGSAM samDesired = KEY_READ | KEY_WOW64_64KEY;
LONG lRetOpen = ::RegOpenKeyExW(
HKEY_LOCAL_MACHINE,
L"SOFTWARE\\Microsoft\\Windows\\CurrentVersion\\Media Center",
NULL, samDesired, &hkResult);
Reference on MSDN:
32-bit and 64-bit Application Data in the Registry