In my experience, the actual package that you are using in PE really does not matter, so long as the "logical" pins you need are there. PE does not really know about the actual pins, just don't use the PE "picture" as a reference for which physical pin maps to the function you are programming.
So, if you set an ADC input to ADC_SE8, PE will generate the code for that "function" not knowing or caring which chip pin it really is. That is to use PTB0 it is the same code regardless of the pin.
Well, you use the RM or datasheet to get the pin out for design, and I don't know that having the correct picture really makes it any easier, because in PE you don't select pins by pin number you select them by pin function (i.e. ADC_SE8). Normally the schematic has the pin number and the MCU function as well as the function of the board.
For example, say PTB0 is pin 10 and the function on the board is BLUE_LED. So you know that to control the blue led, you need to use PTB0 - and as I said in PE you would not select "pin 10" in the property sheet, you would select PTB0.
Also, the modules in the picture (e.g. ADC0) will still be the same if you click on them in the hardware view.
Presumably, the same functions would be used, and the code would be the same regardless of the package.