Is there a way to set a different duty cycle for output 1 and output 2?

You can always use those different waveforms for Out1 and Out2, so you can select waveforms with different duty cycles.

The duty is only valid when you choose the square wave. When you choose a custom waveform that contains a square wave, those have duties built into them, and the duty shown in the user interface is not the real duty.

You can create your own custom waveforms with the duty you want. Before you create your own waveform file, take a look at the waveforms in C:\Spooky2\Waveforms\, opening the .csv files in Notepad, to see the contents of these files. Each waveform file has 1024 lines in it, with values between -1 and 1.

Lets say you wanted a duty of 33.3333. Take the duty, an multiply it by 1024 and round that value (0.333333 * 1024 = 341.33, after rounding is 341). 

Open a text editor like Notepad, or Notepad++ (which is free and shows line numbers), and type in 341 lines with the value 1. Then add the remaining 1024 - 341 = 683 lines with -1. Save your file with descriptive name into C:\Spooky2\Waveforms\, ending in the suffix .csv (be careful with Notepad, because sometimes the file name may end up with the suffix .csv.txt).

Now go into Spooky2, and in the File menu, choose Refresh Waveforms. Your newly created waveform will be in the custom waveform combo box in the Setting tabs.

Note: Do not use Excel or some other spreadsheet to create your .csv files. Excel will add all kinds of annotation to your csv data, and will not be readable by Spooky. Use a text editor like Notepad or better yet Notepad++.

Note: Life is a lot easier when you uncheck the "Hide extensions for known file types" in the Windows Explorer/File Manager's folder options.

For more details, please check the link:
https://www.spooky2.com/forums/viewtopic.php?f=5&t=9668