I wouldn't use them. The idea is to stop the chassis bottoming out, so you could set them without your shocks on, so that they stop just before the chassis hits the ground.
I do believe, though, that they have a un-desirable affect on the handling if the suspension arms travel far enough upwards to the point where the upstops stop further travel.

Maybe a question for Julius - under what circumstances would one wish to use upstops?

Cheers, Mark.