First try at using Matrix view. Watching the SWA Complete Sonar X2 video helps a lot to start off.

What I'm not sure is the best way to go about using Matrix view if you create your own clips/loops on the track, instead of dragging loops from the Browser.

If you record your own midi parts and make them into groove clips, you can drag the clip to the Matrix cell. How do you manage multiple parts ? Do you leave a bar or two and begin recording a new clip on the same track ?

I was going on this route, with some bass and Session Drummer clips. I ended up with the first 20 bars or so as work pad to create clips - so I can drag these clips to the Matrix cells. 

When I'm ready to record the Matrix performance, I will position the Now Time at bar 30 or so.

Seems a bit messy. Are there better ways ?

Thanks.

sometimes i save all my clips by dragging them into the media browser in project specific and classified folders then i can just open a project and drag them from the browser to the matrix. 
i just have some live stuff that i do with pre-rendered audio as background/ambience and some synth intros and outros that i program on the fly combined with matrix view. 
guess it depends on the circumstance. 
one of the other things that i do is i've had a couple of shows where we have a shared drive set up on the performance system and one of the performers will be programming patches for synths throughout the performance which i assign as they come into the shared drive and another person is programming midi sequences and saving those to the shared location, then i'll use matrix to more or less randomly assign the sequences to synths i have set up in matrix and also assign the new patches in the synths we're running. 
matrix has lots and lots of options.  

Sounds exciting on your performance and I'm glad the Matrix view is doing a fine job.

For my usage, while building up midi variations / editing on tracks actively, I do find the regular way working on tracks / step sequencer is more efficient.

Perhaps once I've build up enough variations, I shall save them as regular midi / audio loops, and open up another project to work on the Matrix for trying out different arrangement quickly (using the same soft synt template from the first project).

Glad you found the video useful. As swamptooth has pointed out there's so many ways of  working and variations of settings in the Matrix the possible combinations and workflows are almost endless.

I use it more as a tool for inspiration than anything else, a bit like a musical sketch pad that I then fill out later. I ignored it for years as well, more fool me, I find it great to get ideas flowing.