I'm not sure about the hidden files but if they are system files it is best that they stay on the same disk as the OS. As far as programs go you can create Program Files and Program Files (x86) on one or both of the other two HDDs and install programs on those two disks. You just have to make sure you pay close attention during installation to make sure the programs are installed where you want them. I have moved my temporary Internet files from the SSD to a HDD as well as my SearchIndex, Downloads folder, and Virtual Memory page file.