Dear Nadia,
CasSys is a good option if you want to apply a sequence of substitutions, and if the output of each one serves as input to the next.
If you do not need to chain substitutions, you can use either the normalization step of the preprocessing (cf. user's manual, Section 2.5.3), or Locate Pattern.
If you use the normalization step of the preprocessing, your main graph and all subgraphs will automatically be applied in the Replace mode.
If you use Locate Pattern, you have to explicitly set the mode to the Replace mode, and this mode will apply to your main graph and all subgraphs.
In both cases, Unitex/GramLab does not allow for applying a graph in one mode and its subgraphs in another mode.
The -r suffix at the end of graph names sets the Replace mode only in the case of a dictionary-graph (cf. user's manual, Section 3.8.3), and dictionary-graphs do not make substitutions.
Best,
Eric Laporte