From my experience, you should make sure that the timing wheels line up with the holes in the timing cover, since that's what the sensors measure. Unfortunately, the timing jigs are not always accurate. Back when I was using the old BMW-style timing wheel jigs, I always had camshaft timing error codes and I would have to tweak the timing wheels afterwards. Now that I've switched to using the GAS timing tools, I've gotten the timing spot on with the first try.

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2003 X5 4.6 | 2000 540i Touring

Formerly owned:
2004 Range Rover | 2000 M5 | 2000 540i/6
1995 750il | 2003 Mercedes S500 | 2003 540i/6