The frequencies will be ran under whatever settings were loaded at the time you added the frequency sets.
A preset will just update the settings to a known state (that which was saved in the preset).
If you click on the generator channel control button, it will show you what settings were in effect when you loaded it (provided that it is still running).
For more details, please check the link:
http://www.spooky2.com/forums/viewtopic.php?f=5&t=5102
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