There is no difference, since the SysWOW64 folder will be redirected to System32 for 32-bit applications, hiding the real System32 folder.
Only 64-bit applications will be able to see both, but System32 will be used for 64-bit applications.
There is a good article about the differences and what you have to take care of at MSDN, but I never had to worry, since things are handled automatically by Windows.
Read the
Programming Guide for 64-bit Windows and all its sub-sections, so the confusion should went away.
I would not think too much about there being differences, but start with a simple program and compile it for both architectures.
Now run it and see, if the output is the same for both.
Only check the link above once more for information, if there is something not working as expected.
Start simple and add file system redirection or registry redirection only, if you need it, because you are mixing 32-bit and 64-bit applications.
Keep in mind, that a pure 64-bit environment works the same as a pure 32-bit environment, only mixed environments are resulting in additional code.
I would avoid 64-bit programs accessing 32-bit resources and vice versa, but it can be done if real need is.
