You will likely need a 2 jaw puller or a universal balljoint seporator to remove the balljoint stud from the lower control arm. *Sometimes* these will come out if you tap the lower control arm on the flatened spots or tap on the balljoint stud. The same tool(s) will be used to seperate the upper balljoint from the spindle. The tool you saw is similar to this? http://www.classiccougar.net/ViTech/...s/image014.jpg
If so then to remove the lower balljoint you would use it upside down from that photo and clamp the arms around the lower control arm and thread the ram screw into the ball joint stud

There are usually metal snap/o-rings that hold the balljoints in place. After removing those tap on the balljoint stud and the cup (edge where the larger part of the rubber boot attatches to the joint) to remove the joint. Installation is similar; just carefully tap the joints in being sure not to damage any of the boots or threads.

If they are saying you need a new upper control arm it is probably becasue of the balljoint like you said BUT it could also be the mount bushings OR the arm could be bent. Check your right upper balljoint boot for cracks and wobbles, try and figure out why they said you need a new upper control arm. If the upper balljoint is clearly damaged than the balljoint are removable/replacable.

Hope this helps, Ian