Hello,
AtikBase comes with Atik air pre installed, you should be able to use Kstars / Ekos and Atik air at the same time as long as the camera is connected to Atik Air and not connected in Ekos. So for instance you can control your mount etc in Ekos and the camera can be used on a PC running Atik software using Atik Air as the connection.
Please let me know if this is not the case.
Best regards
Vince