Assuming the application allows you to launch it multiple times, here is a suggestion that would work.
Set the adapter StartMethod property to MonitorAll.
Set the adapter StartOnProjectStart property to True.
Set the UseKeys property to all Windows Forms in the adapter to True.
This allows multiple copies of each form to get matched.
You'll need to keep track of the keys logically so that you'll know which is which.
You'll need to write all your automations carefully so that they keep track of the keys they are working with. If you have multiple automations running at the same time, it can start to get really tricky to figure out which windows belong to which process, so keep that in-mind.
Since calling Start on the adapter will no longer launch the program, you'll need to use the System.Diagnostics.Process.Start method to actually launch the program.
Unfortunately, there is no way to simply create a new instance of a project. You can technically copy a project, although that is essentially making it really tough to maintain (you'd have five copies of everything). To copy a project, you need to change the project's name and ID. You'd also need to change the ID for every .os file. If your project is fairly stable and simple, this actually isn't that difficult to do.