Is it best to replace them with the top up or down?

 

I just replaced mine with the top up and latched. I recommend replacing the hoses too and purging the air out of the lines on a garage floor. Power it up with a spare battery and jumper wires to purge out the air in both directions before attaching to the new cylinder actuators. Then power it up to extend to the "up" position and top off the fluid before installing the whole deal back in the car. No fuss, no muss...