Is this bad for the generator to not have something connected to OUT 2?

Out 2 will run as it's output is set by default to copy OUT 1 unless this is changed in the menu. There is no harm to the generator not to have boost cable or second remote connected. If you want, you can change both values in OUT 2 boxes (OUT 2 Control) from default 1 to 0, as I indicated below so OUT 2 will not generate anything. You'll notice that OUT 2 amplitude (V) circled in red above will change to 0V and there will be no frequency output displayed in generator.

You don't have to do that and this is only to get familiar with adjusting setting in Spooky interface.

For more details, please check the link:
http://www.spooky2.com/forums/viewtopic.php?f=65&t=2751&hilit=protocol.doc

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