The objectives of this part of the two part paper are (i) development of signed digraph (SDG) models for control loops and (ii) discussion of a framework for application of graph-based approaches at a flowsheet level. Further, two case studies are used to explain the methods developed in part 1(1) (Ind. Eng. Chem. Res. 2003, 42, in press) and this paper. The first case study (continuous stirred tank reactor case study) explains the basic concepts of the generate and test method for SDG analysis, generation of redundant equations using algebraic manipulation, and analysis of systems with a single control loop. Case study 2 (flash vaporizer case study) deals with different methods of generating redundant equations and the analysis of systems with multiple interacting control loops.