The competitive market of nano and micro satellites opens perspectives for use of COTS (Com-mercial Off-The-Shelf) electronic components. Current modular electronics design for embedded On-Board Computing systems (OBC) is being challenged by the integration of flexible Systems on Chip (SoC). The deployment of generic avionics and user/payload functionalities on these components is becoming increasingly complex, while Quality of Service must remain compliant with demanding requirements. It is therefore most important to estimate/evaluate those properties as early as possible, regarding a given ap-plication's deployment on a given COTS-based architecture. Model Based System Engineering (MBSE), while a leading practice in architecture description, may still require further study on its use for early evaluation , especially regarding analysis of emerging behaviors and qualitative model-based mapping of ap-plicative functions onto architectural platform. In this paper, we present methods to enhance MBSE design, helping the designer in evaluating candidate mappings and design choices by providing concrete quality measures. We focus on two aspects that were identified as critical in the ATIPPIC IRT project: first, the cost and conflicts in data communications in on-board and peripheral interconnects, which has a bottleneck impact on mapping choices; second, the availability of functions in case of resource failures (from solar radiations), to validate fault-mitigation techniques and estimate the (un)availability of the OBC system. We illustrate the approach on a simplified satellite model, abstracted from a design conceived in the ATIPPIC IRT project.