A "stacked" layout puts the pin and CG the same distance from the PAP.  If you're looking at the ball, then for most people a stacked layout will have the line from the pin to the CG very nearly parallel with the grip centerline (splits the bridge and thumb).  Similarly, if the ball has a marked MB, a stacked layout would have the pin-MB line roughly parallel to the centerline.

It's not the greatest terminology in the world.  You could have a 4 1/2" "stacked" layout that doesn't look like the pin-CG line is parallel to the centerline (put the pin close to the VAL and it looks like a 1:30 drill that went horribly wrong).  Using angles (the PAP-pin-CG/MB angle) is a better system, I think, since you can keep the same angle even moving the pin around.

SH