Hi Tom,
Let me see if I can clear it up:
* Feeder locations are simple locations. No math is applied. The location you set is where the nozzle will go to pick.
* Part height is simply the height of the part as measured, typically with calipers. Part height should only need to be measured and set once per part. A Part should represent an actual physical SKU. If you have a 47uF cap that is 6mm high and one that is 4mm high, those are different parts.
* PCB locations represent the 0,0 origin of the top of the PCB. This tells the machine where to find 0,0 on the board and it performs the math needed to find the individual placements from there. Part height is added when placing a part so that the needle stops at "part height" above the board.
There is no package height - I'm not sure what you are referring to there. Perhaps you mean the Body Height field in the Footprint tab? If so, that is not really used at all currently. You can leave it blank.
Currently the only thing you need to configure in packages is the pads for fiducials. Normal parts / packages don't need any of the footprint data set. They may in the future, but it will likely always be optional.
Hope that helps, let me know if it's still not clear.
Jason