With the 5450 I can not plug in both the lcd via dvi and the d9400 without the lcd going black and the d9400 still displaying no signal.
That's probably because you're not pointing to the right analog output with VMMaker. Your HD 5450 probably has 2 analog outputs. If you select analog_0 you'll be targeting the DVI output, so your LCD will go black as soon as you enable EDID emulation.
You'll need to leave your LCD monitor connected to DVI by now, and the D9400 to the VGA, and select analog_1. The Windows display properties dialog should show two monitors connected after doing this.
If you have issues with the D9400, try using the arcade_15 preset until you figure out the problem. If you still have problems with the arcade_15 preset, start focusing on the cable and connection method, specifically how the sync signals are being managed and whether your monitor can deal with that or not.
I will switch back to the 6450 tomorrow and try again. Should I go ahead and try to do the Atom-15 flash to the card even if the signal still looks like I showed in the video?
No, leave ATOM-15 alone until you figure out VMMaker.
Am I doing something wrong or out of order or could it be the cards, or Windows 7?
It's the process you're following that's probably wrong. You can't follow my guides blindly, you need to understand the logic behind each step and see if it applies to your case.
E.g.: in your video, when you unplug the DVI and then plug the VGA, VMMaker's window suddenly appears on the arcade monitor, true? This shouldn't be the case: that window was showing through the other output! Windows must have re-arranged things automatically when noticing your messing with the cables. You need to avoid that happening.