You're right. You can still select it by clicking, but I find it easier using the nav buttons. It can be difficult to select the missing sprite if there's another sprite right behind it. At least I had that problem with River City Ransom a few times.
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Yeah. Until you've been using it about 25 hours and really start getting the trick to it, it's hard selecting very visible pieces. I've put at least 25 hours into working on the emulator so far and i still find myself clicking 15 times to select a specific piece if it's smaller and surrounded by larger pieces.
I can't even really explain why I'm much better at that now. You just get a feel for exactly where the emulator wants you to click to highlight a specific piece based off of what angle you're looking at it from. It's definately much easier to use Cherkov's navigation method.