Even though there are indeed some decent workflows for arrangement possible in Sonar... we REALLY could use a good, easy to use "Block Arranger" type system. That would make me ever so happy.
 
The way I do this though (and likely similar to other things mentioned) is to record my tracks (audio and live MIDI), set up my loops (groove and MIDI or whatever) and create song segments with the general beats, basslines, riffs I want to be more or less together.
 
So now I end up with "riff/beat/bass/etc 1, riff/beat/bass/etc 2, riff/beat/bass/etc 3... etc" all on their own tracks, routed to the appropriate synths/busses/whatever.
 
Now I have my song segments. I ensure they are all split into those segments ON the measure/beat. That way I can click the top track's clip, hold Shift and select the bottom track's clip to move the ENTIRE segment and all its elements to another area on the timeline.
 
If I need to create room for a section to occur I just lasso all the clips of all the clips that occur on all the tracks after that point (with Snap enabled) and move them en masse further down the timeline to create the necessary gap (this can also be done with that weird Insert Time or Measure or whatever it's called but I just prefer to play Clips Pane Tetris with it all).
 
If I want a beat or part to continue through a segment that does NOT include that part and/or want to mix and match beats/bass lines/elements/etc I can exclude those clips from the move or delete just those clips and replace them with what I want or whatever.
 
I'll usually keep a bunch of elements WAY down the timeline (out of the way of the working area) for one offs or possible substitutes or riff variations (also snipped into measures or segments). That way I can easily drag them into the working area to replace specific segments/parts.
 
Once I have everything composed how I like I'll re-record the live tracks and tweak any MIDI and... well just generally refine the whole thing. For loopty looping that's probably not necessary but I'm trying to emulate "live band" type stuff.
 
The Clips pane really is great for this stuff BUT still a nice block arranger would be better. I'd like to be able to just click on a button at the top of the Clips Pane to select (or define) a section and be able to move/copy/replace/move over/replace/etc segments of the song (using all elements in that range or selected elements of that range)
 
That's mah story and I'm stickin' to it.
 
Cheers.