This is standard. Whenever you install a 64bit operating system you get a Program Files and a Program Files(x86). The Program Files is for 64bit programs that you install. Program Files (x86) is for your 32bit program installs. Basically it boils down to whether the program you're installing is 32bit or 64bit.
What games are you having issues running/updating? When you try patching you could try moving the patch to the folder that the game is installed to. Most newer games shouldn't have an issue patching, is it older games you're having trouble with?