Well, here's what Altera support said:
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hi tom,
i created a simple qii test project that allows us to understand a bit better that those pins are associated with their respective banks and that they are p (power pins) required to be connected to gnd.
you can see this in the tool in three places.
1) fitter report .pin file that e5 is in bank 9a and is gnd, g24 is in bank 7a and is gnd,
2) pin planner shows both pins as a blue p associated to thier respective banks and are gnd.
3) pad view of the pin planner. also associated with their respective banks and are blue p and need to be connected to gnd. notice that this view will show the pins on the edge of the io ring of the bank.
in anticipation that this will give you the info you need, i will place this request in closed pending.
thank you for using myaltera.
-rolando
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i've asked for a little more clarification, since this really didn't explain anything to me. can anyone else make sense of that, and explain it in terms i can understand? :)
i really just want to know if those pins should be broken out from the rest of the 200 ground pins, or not, as far as the schematic symbols go. if they should be, then i really need to have something to add to the labeling (like gnd_pll or something like that). if they not something special, then why are those two the only ones with a bank number listed? i was hoping they would reply and say the bank references in the pin table were there by mistake, and to ignore them. open to suggestions.
tom