I would like to ask if I install 64-bit program into Program Files (x86), will it still work as 64-bit?
Yes. A 64 bit application will always only run 64bit, no matter where it's installed.
However, this will be a non-standard install location for a 64bit program, so would not be something I'd recommend. 64 bit applications should typically be installed to Program Files, not Program Files (x86).