Hi,
You can make the assignment of the pumping wells via the Parameter Association Dialog (right click on a specific file in the Map panel). Here, you can find several ways for Neighborhood Relationship. In the help system there is a fill description of all variables.
In principle, it is always recommended to make a local refinement around pumping wells in order to improve the numerical solution. So, if you are not very far with the model setup, I would highly recommend you to go back to the Supermesh View and reformulate your conceptual model (e.g. include new wells, generate new mesh with local refinements, etc.).
Cheers,
Carlos