Modern embedded systems' increasing complexity and varied safety levels make it hard to coordinate all functionalities within a single run-time environment. Access to more advanced and capacious hardware changes the trend from utilising many separated platforms into one managing the whole compounded airborne system. Providing an appropriate isolation and synchronisation level is achievable only by adapting an operating system with separation mechanisms into UAV systems. This paper introduces Phoenix-RTOS, the microkernel structured real-time operating system designed to be consistent with aerospace standards DO-178C and ARINC 653. The current market offers many counterparts like VxWorks, Integrity 178, PikeOS and many others. These products are well known and used in leading-edge avionics and space projects. However, it is not possible to use them in many low-budget projects due to the high price. The Phoenix-RTOS differs from others and is an open-source project becoming a standard solution for energy, gas meters and UAV systems. In this paper, we focus on the currently designed mechanisms of microkernel architecture for providing a mixed-criticality system, particularly for compliance with ARINC 653. Engineers have been identifying time and space partitioning issues to cope with tight worst-case execution bounds of critical tasks.