Thanks @ibacher , i do think this can be achieved like
Create all the automated automated test in cypress following open concept lab instance. Then in the last feature file and step definition file, this is where we need to add a logic that will pick openmrs qa instance, Inotherwords, we shall be dealing with two instances at ago.
Then with in our tests, we need to call a URL for qa instance and do the other automation remaining, What am sure is, we wont separate them, implying using two instances at go, cc @ibacher how do you see my suggestion.