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I'm not sure whether you'd need to overlay all the ROS packages, so I'm assuming this is not the case.
Your (catkin, I'm assuming) workspace is already an overlay of the system-wide installation and hence whatever ROS packages you have there will take precedence over the system-wide installation (provided your shell is properly configured and your workspace is sourced).
This way, you can place the source of the packages you want to overlay in your workspace, make the desired changes, build and use them without a problem.
However, depending on what sort of parameters you are talking about, they might be configurable via the parameter server and you won't even need to overlay the packages at all. You can set parameters manually from the terminal using rosparam, remap topics, or configure them in a launch file using roslaunch.
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