The Talmud rules that despite the fact that one is obligated to insert “Atah Chonantanu”, the havdalah of prayer, into the ma’ariv of motza’ei Shabbat, one who forgets to do so is not required to repeat the amidah as he will soon make havdalah on wine. The Resp. Radbaz (I, 361) rules that one who missed ma’ariv on motza’ei Shabbat, and is thus reciting the amidah twice at shacharit, as tashlumin, need not say Atah Chonantanu at all, since the wine havdalah will suffice for that, and there is no tashlumin for something that has an alternate remedy. The Magen Avraham (O.C. 294:1) questions this position, noting that Atah Chonantanu has been incorporated into the text of prayer, and certainly before the institution of using wine was in effect, in the above scenario one would have to include Atah Chonantanu in the prayer Sunday morning; thus, even now that the wine version is in practice, Atah Chonantanu must be recited, even if the amidah takes place after the havdalah on wine (even though the amidah need not be repeated if Atah Chonantanu is forgotten).

Similarly, the Tosefet Shabbat (294:1) rules that one who is reciting tashlumin Sunday morning does recite Atah Chonantanu, and does so in the second amidah, which is the tashlumin for the ma’ariv that was missed (see also Pri Megadim, E.E 1, and Shulchan Arukh HaRav, 2). The placement is disputed by R. Akiva Eiger (Chiddushim to Shulchan Arukh) who rules that Atah Chonantanu should be recited during the first amidah, and so too if no tashlumin is taking place (e.g,., if ma’ariv had been intentionally missed), Atah Chonantanu is recited at shacharit.

The Biur Halakhah (294:1) questions this position, which seems to imply a role for Atah Chonantanu at shacharit, on the strength of the above-cited passage in the Talmud. The implication seems to be that havdalah on wine exempts the obligation, and there is no need to recite Atah Chonantanu at shacharit afterwards. Further, the Shulchan Arukh rules (294:2) that one who omits Atah Chonantanu and does not expect to have access to a kos does repeat the amidah; why not simply recite Atah Chonantanu at shacharit? Rather, it must be that Atah Chonantanu was instituted specifically as part of ma’ariv and not shacharit, and the position of those who held that the second amidah should include Atah Chonantanu was assuming that that amidah was a stand-in for ma’ariv.

In defense of R. Akiva Eiger, the Resp. L’Horot Natan (V, 18) cites R. Chaim Brisker’s chiddushim to the Talmud, where he asserts that one who misses ma’ariv on motza’ei Shabbat should recite Atah Chonantanu in the first amidah, because it was instituted not as part of amidah, but rather as part of the first weekday prayer, even if that would be shacharit [Note Chid. HaRa’ah, Ber. 33a, that the rabbis instituted Atah Chonantanu in the first weekday berakhah because of “Z’rizin Makdimin L’Mitzvot”]. (The L’Horot Natan does observe though, that R. Chaim’s position is difficult to reconcile with the language of Rashi (Berakhot 26b.)