Yes. It's best to get the general height of the pickup set first and then fine tune everything with the pole peices and minor pickup height adjustments afterwords.
Adjusting the individual pole pieces can also help with string to string balance. On my Les Paul, lowering the low E pole piece in relation to the other ones cuts the output and the bass slightly. i.e. if the pickup height stays the same, lowering pole pieces decreases output while raising them increases output. But this is just for fine tuning. The overall level of the pole pieces in relationship to the pickup height determines the overall tone. It's just that as you lower the height of the pickup as a unit, you reduce the output and clean up the sound. My first comment really hold true as an overall observable trend.