Often the prefered placement of the speaker to reproduce low frequencies is not the same as the prefered placement to reproduce a realistic soundstage. This means that more often than not a compromise has to be made unless you have complete freedom of placement.
This being said the sub/sat combo is difficult to integrate well (cancelation, crossover slopes, etc).
Read the stuff about the Vandersteen subwoofers if you want to really understand (or be really confused). I personally like stereo subs and good bookshelf speakers when properly integrated.
Good luck!