Open different apps or windows from different stages

@OP

Not sure if you've found the solution but just in case (from MacBookPro):

Each stage can be composed of the windows and applications you include in them. The default, or auto stage, is to group by application, but you can add to it.

Here I have three stages per application: Reminders, Calculator, and Chrome.

If I want to have Calculator and Reminders open in the same stage, I'd select one, then drag (click + hold) the other window onto my desktop

Now, if I open another stage (Chrome), Reminders and Calculator will minimize into the same stage

I've tested with both Stage settings set to open applications "all at once" and "one at a time" and the setting did not have an affect.

Hope this helps.