How to handle multiple instances of same application

Each instance will have a new index number.

Use that as an identificatiojn property. You still need to take care that you track and manage them properly in your test.

I use multiple browsers. I always start the browser with a locator page (very simple HTML file I prepared) so I can find the browser with that open, and then navigate it elsewhere. After that, I track them by their URL in use. If they were all using the same URL, I would have to use the index number of the top level process.