Hi Chuck,
I think all the necessary information is there in the wiki. But obviously it is not presented in a way that has been sufficient for you to build a mental model of what is going on inside openpnp. Sometimes the wiki focuses on details at the expense of the bigger picture. Or maybe you are getting confused by some other features not related to package setup. So let me present an overview and maybe you can point out the concepts which need better coverage in the wiki.
My apologies if this is long and rambling.
Lets follow an example of creating a footprint for a soic package.
The "standard orientation" for a soic package is with pin 1 in the top left, and pin 2 just below it. Hopefully the cad agrees with this, but it does not matter too much if it does not and we get to check this later.
On the Package Footprint tab enter the body size (top left corner of the page). The generator section (top left) makes it easy to set up the pad dimensions for various configurations. A soic package is supported by the

button.
Select pin 1 and press the "Mark" button.
(I dont particularly like that this tab is called "footprint", and the detailed dimensions are for "pads". Those terms really apply to the geometry of the copper pads on the pcb, but here we are really specifying part dimensions not pcb feature dimensions)
Select which nozzle tips will be used with this part, on the "nozzle tips" tab.
Next check the Vision Compositing tab, which is useful because it gives a preview of the package. This shows the body (grey) and pins (white), and pin 1 has a marker. This preview is in the standard package orientation; with pin 1 in the top left.
Next create a part (on the parts tab), and link it to your new package.
There is a minor gui annoyance, but at this point you need to click on an old part, then click back onto your new part. This causes some package-specific details to get loaded into the camera reticule. This only happens on selecting a part now, not necessarily on other changes to a part row.
In the camera reticule (both top and bottom) you will see:
* A blue line, which shows the nozzle orientation. This is the logical "top" of the nozzle frame of reference in the camera view.
* A grey circle on that blue line. This also indicates the logical "top"
* A yellow outline of the package pads. One of those will have the pin 1 marker. This shows the conventional location and orientation of the selected part, in the nozzle frame of reference.
You can rotate the nozzle by dragging the grey circle. The yellow package reticule will always rotate to match.
Next we set up a feeder. With a part exposed, press the button to move the top camera over the pick location. The yellow package details reticule is drawn as an overlay on the top camera image. Hopefully the yellow reticule lines up with the parts pins, and the yellow pin 1 marker lines up with a physical pin 1 marker on the part. If this is misaligned then you need to fix your feeder definition! Either a feeder orientation parameter, or an "orientation in tape" parameter. Note that "orientation in tape" is relative to the "standard orientation" we defined above.
Next mount an unpasted pcb on the machine, load a pcb file, and set up the job x/y position. This can be complicated in itself, particularly if your board are rotated in the panel or you are setting up a double-sided board, but I am assuming this is done. Press the "position camera at placement location" button. This will show the yellow reticule as an overlay on the top camera image. Hopefully the yellow reticule lines up with the copper pads, and the yellow pin1 marker lines up with a silkscreen pin 1 marker on the board. If this is misaligned then your cad has a disagreement about part orientation or center point. This would be unlikely for a soic package, but in my experience it is relatively common for other parts. It is no big deal; just correct the details in the openpnp board file.
Next select the part in the "parts" tab, press "feed and pick" button, and press "Test Alignment". The yellow reticule is an overlay on the bottom camera image, and it should match exactly with the part. The yellow reticule pin 1 marker should match any pin 1 distinguishing features visible on the bottom of the part.
The "Test Alignment" button has a "placement angle" field. If this was zero, then the blue line is vertical at the top of the screen and the part is shown in its conventional orientation. To be precise: the part was presented at approximately zero degrees orientation (maybe that involved rotating the nozzle after it was picked from the feeder), the vision measured the angular and position error, then the nozzle had a tiny movement to correct.
If you change the placement angle and press the "test alignment" button
again, then the nozzle rotates, vision is processed at the new rotation, and the blue line moves to show the top of the part's frame of reference. Everything has rotated. During a job there are various factors that affect the angle at which vision is performed, but that doesnt have any consequences during this setup stage. The key detail is that bottom vision might be performed at any angle.
At this point I would advise turning on part size checking, using PadExtent method. This is an automatic check that the pins found by bottom vision match the size of the yellow reticule. This is off by default for backwards compatibility reasons.