interact with multiple Desktop and web application to complete single test

A single test in TestComplete can involve as many applications, web and desktop, as necessary in order to complete the test.  It's simply a matter of invoking the necessary application and making sure that the objects are properly mapped.  In a previous job, I incorporated at least 5 different applications within a single test.

While I don't recommend necessarily keeping the test "as-is", you can try simply recording a basic test utilizing all your applications.  This should give you at least a starting point for seeing how TC interacts with applications.

Yep. I'm the same. Often use a combination of Web and Desktop in a single test suite. And multiple browser instances within tests. As long as you are easily able to tell them apart, it should be fine.

Multiple instances of THE SAME desktop application, or multiple websites, all in the same browser and using the same URL, are more problematic.