I would do so:
In Salomé/Geometry you can create consecutive volumes+faces+curves. You may unify these to 1 item by making a "Compound". Then create groups corresponding to your coming element groups. Basically one group per combination of Modelisation and Element characteristic (Material (1D,2D,3D), wall thickness(2D), section type (1D)) and groups for the geometry where you intend to apply constraints/loads.
In Salomé/Mesh create a mesh and in this mesh create submeshes corresponding to 3D, 2D and 1D elements.
Calculate the mesh and then create Groups from geometry (Elements/nodes as required) per your definitions in the Geometry module.
Then export MED file - if you want (and what you asked) - or go to Salomé/Aster set up your calculation with this mesh. You should be able to address the different groups from within Code_Aster where you combine different elements (e.g. coque and poutre).