If you are going to be playing 6 deck blackjack, PE is not nearly as important as BC (playing efficiency and betting correlation).
The reason for this is that in 6 deck, the swings in player advantage occur much less and are more gradual. This does two things: you won't encounter nearly as many extreme counts and swings in player advantage are more gradual.
Due to the lack of extreme counts, many play variations will almost never be used. This negates the benefit having having more accurate play variations.
Due to the gradual changes in player advantage, you need to be able to recognize your small advantages more accurately, as they occur less frequently and are less obvious.
This means being able to bet more accurately in a 6 deck game is much more important than varying strategy. According to Professional Blackjack by Stanford Wong, "Varying basic strategy with the count per deck improves on basic strategy only by a small amount...Most of that improvement is due to taking insurance, standing on a hard 16 against 10, and standing on hard 15 against 10."
If you go for the counting system with the highest playing efficiency, you will sacrifice a lot of potential profit playing 6 deck games. Both Hi-Opt II and Uston APC have BC's of .91. One is a level two system, the other one is a level three system. To bet accurately on a 6 deck game using these, you must side count aces. This makes for a very hard counting system indeed.
On the other hand, you can settle for a much easier counting system with a much higher BC while sacrificing the rather unimportant PE. Let's take a look at the standard, Hi-Lo. Hi-Lo is an easy level one count, but it has a .97 BC, .06 more than either of the two high PE systems. This means it is a much better choice for shoe games (4, 6, 8, or more decks....though I've never heard of more than 8 decks).
If you want to continue with a system that uses a high PE, you should find some single and double deck games. If those aren't a great option, stick to systems with a higher BC.
For reference, here is a list of counting systems that includes both the PE and
BC values:
http://www.qfit.com/card-counting.htm