Tips for DS ripping?

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Unfortunately Desmume only shows the sprites through the OAM viewer as they appear on the screen, so if they get overlapped or cut off, then OAM doesn't help with getting the rest. You may be able to use the Tile Viewer for that kind of stuff though. (Under "Tools")

Also, as far as I know there aren't any shortcut hotkeys for disabling the layers, but I'll search around a bit more.

I've never had the cross problem when using the touch screen, could you provide a screenshot?