Mincha, or this part of Mincha, begins with three steps. The first step, we said, was Hamatzah; the second step was the Korban (offering) Tamid. We mentioned the Korban Tamid, which is a daily Korban: we brought one in the morning and one in the afternoon. The third step, before Ashrei, is the mention of the Ketoret (the incense), where we list the whole Ketoret, the whole sacrifice that was brought in the Beit Hamikdash, again once in the morning and once in the afternoon.
The issue is that, according to some, the Ketoret should really come after the mention of the main service of the afternoon, which would mean that the Ketoret should be said after the Amidah. The Rama says that the Ketoret should be said after the Amidah because he considers the Amidah to be the afternoon service. Therefore, the Ketoret was brought after that afternoon service; it was the last thing, pretty much, so he brings it after the Amidah. However, our custom is definitely to do it before the Amidah. Why? They bring it from the Zohar, and the Chida brings us as well a big Kabbalah (Jewish mysticism): it's good for our tefillah (prayer) to have that introduction.
You have the LaMenatzeach we mentioned, you have the mention of the Korban Tamid, and then you have this list of the Ketoret, part by part. You say the whole thing. It's very good to go into the Amidah; you're getting rid of certain different issues before you get into the tefillah. It's a big Kabbalah, and it makes your prayer more accepted and therefore more powerful. So, even though there's an argument to be made for saying the Ketoret after the Amidah, if a person is late, he should say the Ketoret after the Amidah, because there's not much wrong with that. Maybe even, in a certain sense, according to some, it's better. But our custom is to do it before, and it helps with the power of our tefillah. Have a great day.