In the context of the growing interest for systemlevel testing for radiation effects, this paper presents the development of different levels of software and firmware instrumentation with limited overhead that can be statically or dynamically added to the application under test in order to provide different levels of observability of radiation-induced single-event effects and total ionizing dose effects, as well as to improve the component-level diagnosis of failures observed at system-level. The instrumentation levels are described and applied to a digital control-loop application implemented on a Zynq7000 based commercial system-on-module. A first set of results obtained under high energy protons is presented and discussed.