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Automatically starting application show up on the 1st desktop. Is there a way to make them appear on a different (2nd, 3rd, etc) desktop?

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If you're using compiz (desktop effects), yes.

Just install the CompizConfigurationManager, it has a plugin which allows to set such rules. I don't know what it is called exactly, but you'll sure recognize it if you see it (something with Window Location or Place Windows).

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If you want a specific application to end up on a specific workspace, you can use Devilspie :)

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