Not sure what you mean by onboard graphics - it's emulated AGA I use 99% of the time. The EeePC itself has some crappy Intel 945 graphics chip.
Yeah, I had a feeling this little netbook wasn't beefy enough. Too bad though, it's a nice little machine otherwise. Well, still good enough for running DPaint 
He means are you using RTG graphics in WinUAE. It uses the on-board graphics adapter on your motherboard to display the RTG graphics and takes a lot of load of the emulator (it doesn't have to emulate the Amiga's custom display chips).
UAE then becomes a LOT faster.
You need to install Picasso 96 and some other stuff to operate this way.
But for displaying demoscene stuff RTG won't work - demo stuff almost always needs the native chipset.
