The vast majority of native speakers never use the word "whom." (Outside of set phrases like "for whom the bell tolls.") You could safely forget that it exists and devote time to studying other facets of the language.
The "rule" you are asking about is a compromise that many educated people have made in the recent past (see William F Buckley, Jr. for one). The idea is that insisting on using "whom" in all cases is outdated, but that one should still use it after a preposition.
So, "Whom are you waiting for?" is traditional correct.
"Who are you waiting for?" is the normal speech used by most speakers. Those following this "rule" would say this.
"For whom are you waiting?" would also be used by those following this "rule," since the "whom" immediately follows the preposition. But it is unlikely for most native speakers, because it sounds overly-formal.
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