Why do I have to Apply Trimming twice?

I have a long clip with a big blank section in the middle. I decide I want to split this into two clips. (They are a single clip because it was recorded in a single take, but it's really two separate things.) So I Alt-Click in the middle to split it into two clips. When I do this, each of these clips now has a tiny corner chopped out of it which I don't know what it's for. Then I need to remove the blank space in each clip, so I right click on them and select Apply Trimming. The first time I do this, what happens is that little chopped out corner disappears, but no actual trimming has taken place. Then I have to Apply Trimming a second time to get the actual blank space to disappear. What's going on here?

I see. I never use slip editing.
 
Is there a way to cause Sonar to automatically combine, split and trim clips based on the contents? I do most of my work in PRV, but then when I need to look at the project in Track View, I've got a hundred tiny clips overlapping each other or else I'll have long clips with huge amounts of silence in them, or both. Basically, the clip boundaries bear no resemblance to the actual music in the project I realize I could open take lanes to help with the overlapping clips, but then I lose a lot of vertical space. And many of those take lane clips could still have empty space in them. Truth is, I don't care much about clips at all. But if they better represented the actual note info, they could be useful when I want to see which instruments are playing when, which can be a lot more difficult in PRV with all the overlapping note info.
 
I'd like to be able to select a region and say "If there's a break of x bars or more, split into separate clips, otherwise combine into a single clip and trim everything." Then my Track View is going to be nice and neat and will accurately reflect what I actually have in the piece. 
 
I'm dating myself here, but in very early versions of Cakewalk, like early-mid 90's, before there even was such a thing as clips, it would simply show a big dot if there was any midi info in a given bar on a given track. Of course, you couldn't drag these dots around or operate on them as a group they way you can with clips, so they were much more limited, but what they DID do was what I'm talking about here. You could easily and accurately see where you did and did not have events in every track. 
 
Switching to Notes instead of Clips in Track View isn't much better, because there's no intelligence behind vertical positioning of events, and I have to resort of Fit Content on every track one at a time, and if I'm using keyswitches, that content gets mercilessly squished to a few teeny pixels anyway. And those tiny lines are the only feedback I have as to whether there's midi datea in there, often really hard to see.
 
Anyone know of any way I can solve this problem without my current workaround of constantly bouncing and trimming clips for no other purpose than so that I can see what's really going on?

I would personally use the "Bounce to clips function".
Its almost the same thing as apply trimming but it can also heal clips. The down fall of Bounce to clips is you can only do one clip at a time if you want to create separate clips on the same track. If you select multiple clips on the same track and use Bounce to clips, they(their gaps) will be healed.
 
I would like to introduce an interesting perceptive though. Before slicing all your midi clips up in to pieces,
I would highly suggest making a back up of your midi clips (in one whole clip).
If something were to ever happen to your Sonar project (weather it become corrupt, wont open, keeps crashing).
You have no way to recover those midi files/clips. In other words, all that work you did...its gone.
If you save 20 little clips that go on one track, its a nightmare to re assemble them on one track at a later date.
Its much easier to have one whole track to import to a new project.