Paper presents research framework based on methodology of knowledge acquisition via visual structured analysis of the domain. The methodology includes formal procedure and special techniques of knowledge stratification and detalisation. Described approach is implemented in computer programs, that may be used as special cognitive tools, helping domain experts to investigate the domain knowledge through visual design of concept maps of knowledge bases. The paper also discusses how ontologies can be specified at the knowledge level using the set of graphical intermediate representations. Special software tool implementing visual knowledge engineering techniques and principles is described in the paper. In this paper, we also present the CAKE as a software tool to specify ontologies and concept maps at knowledge level. Its multilingual generator module automatically translates the visual specification into targeted knowledge representation languages. CAKE may be also effectively used for visual hypertext design and development of hypermedia applications on WWW.