Actually, Cake needs to have an editor built-into SONAR, including for the matrix. Put a performance (midi or guitar or drums) into a cell, top and tail it, sync it to the beat. Most of the tools are already there, just not implemented as needed. My idea is to perform songs live by playing the matrix. So I've been starting songs with various loops (prefab or heavyocity performances, etc), freezing 4-12 bars of various lines, then getting those audio clips synced back to the song temp and them using them as matrix pads.
It is a rather arduous process. It seems (to me, a non-coder) a hopefully simple process.
And my crack about guitarists was in fun. SONAR seems geared toward musicians with a PC and guitar who want to do full bore band-type productions without being able to record an entire band at once. While Cake have added a lot of functionality to that basic concept, the Matrix is seen mostly as an arrangement tool rather than an end in itself.
It will make a great looper tool, either for Cake or someone else. One has only to look at Cake's own Scratchpad (for iPad) to see the possibilities, not just for recording but live performance. Scratchpad, without the limitations of importing and the # of Pads, should be grafted into SONAR or at least a stand alone app for PC.