How to reorganize the workspace

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As long as the two systems use the same ROS interfaces for their communication, it shouldn't matter too much how you organize your development process. You have two main options for using separate workspaces:

1. Have each workspace depend on a third separate one that only contains the interface definitions
2. Have each workspace including a copy of the interface definition source (i.e., two clones of the repo). Just make sure if you change it in one workspace to bring the changes into the other workspace as well.

If you'd like more info/guidance it would help to expand your question to more concretely describe your scenario instead of only talking generally.

create two different workspaces, each for the single robotic system (They could talk together? How?)

catkin config --extend ~/some_ws/devel/ could be a nice way of underlaying one workspace to another workspace. Check if this is something you might be looking for.