Which Mizbe'ach is the Pasuk referring to?
Rashi: It is referring to the Mizbe'ach ha'Ketores which stood before Hashem in the Heichal.
Where did he go out to?
Rashi: After standing between the Paroches and the Mizbe'ach (in order to sprinkle towards the Paroches), he moved out to a spot on the far side of the Mizbe'ach in order to sprinkle on the Mizbe'ach, beginning with the north-eastern corner.
How did he atone for the Mizbe'ach ha'Zahav?
Rashi: By mixing the blood of the Par and of the Sa'ir and sprinkling them together, as prescribed in the following Pasuk. 1
Why is all Avodas Yom Kipur Kosher only through the Kohen Gadol?
Moshav Zekenim: Yom Kipur is like the world to come. Just like Micha'el atones above, Aharon atones below.
Rashi writes that he mixes the blood of the Par and of the Sa'ir and sprinkles them together. Even though there is more blood of the bull, the blood of the goat is not Batel. How does R. Yehudah learn from this (Menachos 22a) that Min b'Mino is not Batel? Perhaps he takes from the bull only as much as the goat's blood! Also, perhaps it is not Batel because it is Kavu'a (fixed)!
Moshav Zekenim: Kavu'a only applies to something important and recognized. (He left the first question difficult.)
Griz (22a): The Yerushalmi holds that one must mix all the bull's blood. (There is no source that the Bavli argues.) Sefas Emes (22a) - we must say that we mix all the blood, for we must put the Shirayim on the Yesod. If some was not mixed, the Shirayim from what was mixed are not Shirayim from what was not mixed.