The lowers are the hardest. Torch the old ones out, and clean up the housing for a good burr free fit. Spray a little pb blaster or other lube in there, insert ball joint, then find a piece of tube that fits over the body of the ball joint (needs to be the right size so you don't ruin the socket surface at all), slide it over and then lower the rig every so slightly so the piece of tube you slid over the joint rests on a block of wood with a little pressure, then "pound" on the housing to get the joint in there. Keep lowering the rig a little more and "pounding" as it slides in to exert some pressure.
If you use this method, all your "hammering" is done on the housing itself and you don't risk damaging the joint.
Screw those stupid ball joint presses. I've NEVER had one work as intended.
And yes, you need to get it all the way in otherwise things will never line up right when you put the knuckle back on.