32bit apps can query the 64bit registry, using the appropriate security and access rights options such as KEY_WOW64_64KEY (0x0100).

Similarly KEY_WOW64_32KEY can be used for 64bit apps to read/write the 32bit registry without having to have knowledge of how the Wow6432Nodes are arranged .

These mean that a 64bit aware app, whether compiled as 64 or 32 bits, can access the alternative view of the registry.

http://msdn.microsoft.com/en-us/library/ms724897(VS.85).aspx
http://msdn.microsoft.com/en-us/library/ms724878(VS.85).aspx

For example if you have both 64 and 32 bit copies of Python installed then a Python app running under the 32bit copy of Python can query the location of the 64bit copy of Python using code like:
key64 = _winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, "Software\\Python\\PythonCore\\2.6\\PythonPath", 0, _winreg.KEY_READ + 0x0100)
_winreg.QueryValue(key, "")

C code can do similarly.