don’t worry, you will be fine.
only way the 8400GS would be used if it was primary video card, which also means your monitor would have to be hooked up to it. each time you would watch a movie you would have to switch from 8400 to 8800.
your system will do just fine.
BTW, yes you can install different video card in extra PCI-E slots, just can’t use two different cards together in SLI.
software doesn’t matter, but it might sound weird, i get better picture quality playing the ripped movie in WMP11 then playing it PowerDVD Ultra.