If you look in the Resources/Template/Document Templates. You will see it as a choice in the tree, under packages. The functionality feels a bit unfinished to me for a couple of reasons:
1) It only allows you to include realtionship matrices that are built directly from a package. If you use a model search for the matrix, there is no way to include it (from what I can see).
2) When you do use packages for the matrix, it shows up twice! Once for each package in the Matrix.
To me, it makes more sense to include them in the Model/Resources node (which is where Matrix Profiles show up in the UI anyhow) and perhaps allow a filter of some sort one which ones are displayed.
One other nice feature, or approach, would be to put a RelationshipMatrix stereotype into the tools for the Documentation model. This object could use TaggedValues to specify either a profile name, or all of the Source/Target/Type, etc. inputs to the Matrix. You could then you could then just add this to a model document and thus be specific about where you want specific matrices to show up.