As Freddy says an all-up is really 2 or 3 or 4 different bets (depending on how many "legs") - it is just that the TAB is placing the 2nd and subsequent bets for you (if you win). The TAB certainly includes the total turnover in their figures, not just the original bet, and they take their commission off of every bet.

The problem I see with using only the first bet for POT is you are going to get a distored view of your real success depending on what order your winning bets come in.

For example lets say we make 9 place selections at the start of the day and group them into 3-allups. Now 6 of our selections win paying $2 each (just keeping it simple for the example).
On single bets, level stakes our profit is $3 and POT = 3/9 = 33%
Now with the allups we could have either no wins, 1 win or 2 wins depending on the order of the winners (eg WWL,WLW,LWW or WWW, LWW, WLW or WWW, LLL, WWW). Each allup will pay $8 if it wins (2*2*2) so we will either have a loss of $3, a profit of $5 or a profit of $13. Therefore our POT is either -100%, 166% or 433% - makes it a bit hard to judge how good your selection system is - you are either really disappointed or you think you have the best thing in the world.

As I said before you obviously need to keep records of the allup totals but you should also record every individual bet and work out your POT based on the individual bets - otherwise you have no way of knowing how good your selection strategy is and whether your allups are helping or hurting your bottom line.