This a very simple procedure. When kanji has multiple onyomi, you incorporate a character from the movie associated with the reading into the scene. For example, when I remember two readings for "child" (the one with the kunyomi 'ko'), I learned it primarily as 'SHI'. So I put the kanji in my location and learn it. But it also has a reading of 'SU'. When this happens, I simply have to take a character from my movie for SU, and incorporate it into the scene to remember both readings. Simple and effective.
A different way would be to remember the kanji in both movies, but it's a bit weird remembering two locations for each kanji.
Added: So when I refer to a 'character' that you incorporate into the SHI movie from the SU movie, I mean a movie character. As in, a character played by an actor.