We need to run ccmsetup.exe instead of msxml6_x64.exe to install SCCM client on Windows 2008 Server 64 bit machines.
After installation (It will not give any wizard, background installation) check in control panel ->View 32 bit control panel Items. Here we can see configuration manager. And we need to wait some time to reflect client status YES and Approved in SCCM server. (Just run update membership collection from server)