Daedalus is a system-level design flow for the design of multiprocessor system-on-chip (MP-SoC) based embedded multimedia systems. It offers a fully integrated tool-flow in which design exploration, system-level synthesis, application mapping, and system prototyping of MP-SoC architectures are highly automated. In this paper, we describe Daedalus from a software perspective, explaining its supporting software infrastructure and the way the various tools interoperate. Moreover, we discuss the lack of support for achieving tool interoperability that we have encountered during the development of Daedalus, and present several ideas of future research directions to address this issue. More specifically, we argue that a so-called Common Design Flow Infrastructure (CDFI) for system-level design flows is needed to improve and stimulate research and development in the area of system-level design methodology.