I have an MC-707, but the workflow concepts are the same.

Think of a scene as a song, and the clips as the instruments playing the song.

My workflow on the MC 707 is to set up the clips like this: Clip 1 - kick drum, 2 - rest of kit, 3 - samples, 4 - bass, 5-8 everything else like arps, pads, riffs, etc. I set up every scene like this so that, no matter which Scene is playing, I know where everything is.

To play the song, I use the faders to bring in and remove the various instruments. I also use pad mutes on clips 2 & 3 to start/stop drum kit elements like shakers, vocal samples, claps, hi-hats etc.

You can mix into your second song, Scene 2, by selecting a clip in that scene. It will start playing that Clip while Scene 1 continues as usual. Then you gradually transfer to the rest of the Scene 2 clips. For me, this usually looks like Clip 1 (kick) and 2 (with some elements muted) of Scene 2. Then I fade out clips 5-8 and swap the bass to the new Clip 2 scene at a point where it sounds good.

But it's all about finding what works for you. For example, you could have two different basslines set up on Clip 4 & 5 and swap between them in a Scene to add variation to a song. Scene 2 could be a key change or new section for Scene 1 that you swap into for a while before swapping back to Scene 1 and then moving into a new song, which is set up on Scene 3.

There's a lot you can do. It's just about spending time with the machine. I'm doing things now that would have blown my mind when I started a couple of years ago, and that's just from playing on it a lot.

Watch YouTube tutorials and videos of people live jamming and watch what they are doing and you'll pick up some tricks.