I have an XGK, 80's vintage.
Just shut off the valve at the pump and it should burn whatever fuel is left in the line; I don't recall there being any left over after doing so, but the new ones are a slightly different design.

Not sure what you mean by fuel on the pump; just close the valve and disconnect the pump from the fuel line when you are done using it.

I put the stove in my pack and the fuel bottle in an outside pocket with the pump in the bottle.

You avoid spilling white gas by being careful like you would with any liquid. I've carried two fuel bottles and it hasn't been a problem. Just be careful when you prime the stove-you don't want too much fuel in the priming pan otherwise you'll have a pretty good sized fire for a minute or two.

You don't need a pad under the bottle, but putting the whole stove and bottle on a piece of blue pad is a good idea. It stabilizes the stove. The fuel won't freeze but the pad keeps snow off the stove itself, which is a good idea.

White gas is cleaner than kerosene.