Ideally, Musaf should be davened before the seventh hour of the day (1:45pm). Since the Chazzan cannot move out of his place to bow at Aleinu, he should stand at a distance from the Shtender (podium), to allow him some space to bow.
In those communities where they blow Tekiot in the silent Amidah, the Baal Tokeiah knocks on the Bimah beforehand to signal that he is about to blow. One should pause to listen even if he is not yet up to the corresponding place in the Amidah. A Makrie is not used during the Musaf Amidah.
The paragraph of Misod (beginning of Chazarat Hashatz) is recited by the Chazzan and not the congregation. Some have the custom to stand for U’Netane Tokef. The Chazzan recites the entire Aleinu – including the second half – out loud. The congregation quietly recites it word for word with him, bowing at V’Anachnu Korim, and continuing until Hu Elokenu Ein Od. At that point according to some, they begin saying the Pesukim of Atah Haraita, as printed in the Machzor. The subsequent paragraph (beginning Achilah) is recited by the Chazzan only.
When one bows, his head should reach all the way to the ground. One may not bow directly on a stone floor, but rather, should prepare mats or any other covering upon which to bow. Some do not bow directly on any surface without a covering. The Chazzan must keep his feet together during the Amidah. He should therefore be helped up after bowing at Aleinu.