It is not usually recommended that you run an RPA bot from a machine in-use by someone. Automating desktop applications can sometimes require that they be activated or brought into focus to execute certain steps. In addition, the applications themselves might set focus to themselves for certain operations. This would make it disruptive to a user of that machine.
That being said, there are no specific settings to run an automation in the background. If your applications can be automated when minimized, then you can simply automate that step after starting them and then they would remain minimized unless otherwise told not to be. You can also create a Windows form and add a TabbedReparentContainer control to it. This will place the applications you are automating inside the Windows form. This might keep it even more out-of-sight.