No, you may only have one instance of Pega Robotics Runtime running at a time for one user of the Windows session. This is for both RDA and RPA.
Separate your solution into separate projects. Each project should operate on a specific adapter or application with automations and other parts specific to and only operating on that adapter. Your developers would then agree on their automation inputs and outputs so that they are consistent. In your controller project (the one that references the others) is the only place where the developers work would need to be interacted with.
See above. Create a project for each adapter and test those automations individually. When you are certain that your automations work, you can simply integrate them with the controller project and know that they will work.