if you have an example script you could name, we might be able to help. Look at the log file, and it should have at the top a listing of the variables being used, and you should be able to see the different variables
The issue is that if the script and project is not designed for an X64 build (and does things to know if it is a 32 bit program, and so should be used instead inside the script), then it won;t have the logic to put it in the X86 directory.
Still not sure (as peter mentioned) why you need to boot an X64 based OS...Doing a temp disable of the secure boot shouldn't be an issue, and not sure why you need optimized programs??? Remember a PE environment is not the same as the full OS, and shouldn't be used instead of a full OS...
But as mentioned above, *IF* the project supports it - AND the script supports it, then it's possible to encode it to go to the right placed based on logic to determine the type of source...
Scott