I too would love to use Matrix View for song arranging but
it seems to be full of bugs and nobody here can shed much light on it. Like the Step Sequencer, it seems to have been added in to make sure Sonar had feature parity with some of the other DAWs, but fixing and improving them is not a core priority because few people seem to actually use these features.
I have 2 methods I currently use to arrange songs within Sonar, neither ideal. The first is to drag around all the clips to select them, drag them to the new position, followed by manually moving any markers. The second method is to select the area I want and cut it out before pasting it elsewhere - this often goes wrong if I'm not careful to make sure I have every track selected because everything after it can be moved along by different amounts.
I just realised the other day that the clip-grouping thing would help me a lot with the arranging so I'll probably do more of that in future. It's just a real shame that markers can't be drag-selected like clips. It's probably also best to slip-edit all the clips to measure boundaries first so that you don't end up with weird crossfades. You can manually apply crossfades later once the song structure is chosen.
If I want to re-record a section, I just select the lot and mute them (press K, I think). The new recordings will go in a different take lane. Then I can listen to each take and decide which one to keep. Make sure you're in Sound On Sound recording mode, not Overwrite.