Looking at your X config, you're trying to do dual screen rather than TwinView. I'd look at TwinView, which is an nvidia driver specific feature, first. That makes a single coherent screen across multiple displays. With multiple screens (the way you have it set up), they are pretty much segregated, so you can't move apps between screens or span them (although there are some reasons for preferring that config). Also, on your second screen config, why do you prefer 640x480@60 Hz as your first resolution choice? Also, why do you have all of those modelines explicitly specified for your digital display? It should be getting that info from EDID with just the resolution specified in the Screen section.
To see if 3D acceleration is working, run nvidia-settings and check the OpenGL/GLX information tab. If GLX information shows "Direct Rending: Yes," then 3D should be working.
After that you probably just want to look at setting up TwinView
. My TwinView setup looked something like this:
Identifier "Generic Video Card"
Option "TwinView" "true"
Option "TwinViewOrientation" "LeftOf"
Option "SecondMonitorHorizSync" "31-81"
Option "SecondMonitorVertRefresh" "55-85"
Option "MetaModes" "2560x1600,1600x1200 @1600x1600; 1280x800,1600x1200 @ 1600x1600"
Device "Generic Video Card"
Monitor "Generic Monitor"
Modes "2560x1600" "1280x800"
That was when I had a UXGA secondary monitor sitting to the left of my main display.