Research on Comprehensive Evaluation Methods has become increasingly widespread. These methods can be applied to many different systems with a wide range of system characteristics. There is a great deal of flexibility in the choice of qualitative and quantitative methods used in the evaluations, however there is a lack of guidelines for proper application of these methods. Evaluations can be performed by many different methods, however the results are often different for different methods. So the question becomes, which method is best? This cannot easily be answered. Practically, however, by following some key ideas and by having a good understanding the available scientific methods, an effective evaluation can be still be made. In this paper we will study the key characteristics of the comprehensive evaluation process and its application to practical issues. We will show the steps towards making a suitable choice of scientific evaluation methods, making the evaluation process more efficient and the results more effective.