For anyone coming to this page later, the solution can be found in this thread
viewtopic.php?f=22&t=120294The simple answer is that when you add a new Media In node, there's a control called "Layers" in the inspector tab that allows you to select which video layer the media in corresponds to. So if I wanted to add a new clip to the comp, I could open the fusion comp as a timeline, drag the video file onto a new video layer (for example the 2nd layer), trim it up how I want it, then go back to the overall fusion comp page, add a Media In node, and select layer 1 in the inspector tab (it starts at 0, so selecting 1 means the 2nd layer in the timeline).
I've been searching for this solution for weeks! So glad I finally figured it out!