In general, standard ROS practices apply. Write your code for ROS, put it in a package, and then build it in a catkin workspace.
For Aqua, your code should go in the workspace at /home/aqua/catkin_overlay_ws, on the vision computer. Put it under the /src directory as usual, and build the workspace. The only thing to be sure of is that your /devel files properly overlay the catkin_base_ws, which contains the base aqua code. To make sure that this is the case, the environment from catkin_base_ws should be sourced when you build the catkin_overlay_ws.
To confirm the overlay is correct, source the setup.bash from catkin_overlay_ws, then run a
and see if packages from catkin_base_ws are listed. aqualaunch is one good one to look for.
See this ROS tutorial for more information on overlaying workspaces.