@Wicke2d ,
At startup of windows? Yes, there are multiple ways.
You could create a .bat which runs two instances (ie, it calls c:\Program Files (x86)\Notepad++\notepad++.exe twice, at least one of which with the -multiInst option, or having the always-use-multiple-instances setting on in your Notepad++ config), and put that in your Startup folder (search the interwebs to see how to add something to the startup folder for your particular Windows version).
Or you could use Task Scheduler to create a task that runs two instances of Notepad++ (again, with the -multiInst or the preference equivalent mentioned above)
I have a dual desktop setup
I, however, don’t think that either of those solutions would be able to put a separate instance on a specific Desktop when you first boot.
I want to say maybe you could do it with calling a different session from the command-line in each, but I don’t think that would be able to automatically run them at bootup. Maybe someone else has some ideas.