I noticed in the Settings tab it set Out1 to a Square wave with Inverse+Sync selected. The notes for the KHZ preset say Square wave, 100% positive Offset, and Amplitude of 9.5. Should the Waveform be set to Follow Out 1 or left at Inverse+Sync?

If using Out 1 directly, the use of Inverse+Sync or Follow Out 1 does not matter as Out 2 is not in use.

If using a boost to combine both outputs, then you must use Inverse+Sync in order to combine the outputs together correctly to produce a waveform with twice the amplitude.

If you use Follow Out 1 with the boost, then the two waveforms will be 180 degrees out of phase with each other (a result of the boost wiring) and will cancel out resulting in no waveform produced.

Therefore; you would use Follow Out 1 is if you are going to use Out 1 and Out 2 at the same time, but with different devices attached to each output.

The other reason to use Follow Out 1 is if you are making Out 2 different in some fashion and prefer this over Inverse+Sync. Both version result in a very similar output as long as Out 2 does not match Out 1 frequency wise. The primary difference between the two options is whether the output of Out 2 is normal or inverted.

Remember that under the boost, the output is reversed by the wiring, and thus we need to invert it once more in software so that the resulting output is not 180 degrees out of phase with Out 1.

It is also the reason we use 100/-100 for the offset, as when we invert Out 2, the -100 offset becomes 100.

For more detail, please check the link:
http://www.spooky2.com/forums/viewtopic.php?f=71&t=6431