Am I correct system settings like ‘midi echo off’ and ‘multitrack off’ are reset each time a new song / project is made?
All settings are project based. So when you load a project, it also loads the settings it was saved with.
You can make the current settings as “default”. So next time you start a new project, the default settings are loaded.
Settings -> Save -> Save Settings
Save settings currently stored in flash memory. Settings options will be auto-loaded at Pyramid startup.
Hope this helps 
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Oh yes,
I overlooked this in the manual, thanks!