So the netbook will be using a separate touchscreen?
I'm not sure what you mean by a 'touchscreen controller'. Touchscreen controllers go between the USB interface and the touch glass, but it seems you're referring to some sort of touchscreen headunit?
There are probably touchscreen kits for your netbook, that's an option, unless you really don't want the netbook up front.
I'm docking, not hardmounting my One, so I'm manually starting it. I'd assume you'd want to wake on hardware activity (like wake on lan or usb etc), if it was hard mounted.
If you're not using an external amplifier, you would keep the headunit.
As for frontends, Centrafuse is fairly easy to set up but costs $$$, RideRunner is free but trickier to set up, and that's about as far as my knowledge of frontends goes.
The choice of front end is basically personal preference.
If you're only doing music you could get away with a simple media player instead of a full frontend, but then again you need big buttons for touchscreen...