I agree, the best solution here would be proper UI support for editing advanced settings:
Until that’s implemented, the simplest solution is to use environment variables for your custom advanced settings.
If you’d rather edit the system and library settings files, just set this environment variable to true: PS_START_PAUSED=true
After you go through the welcome and settings pages, shut down PhotoStructure, edit the setting files to taste, unset PS_START_PAUSED, and restart PhotoStructure, at which point sync will start for the first time with your desired settings.