Hello,
Swat does not operate based on "coordinates", but rather on landscape positions. Your HRUs (that are a combination of soil, LU, slope) are VIRTUAL. Meaning, that you CANNOT map them. Yes, QGIS will show you their "location", but that is not how one should think. As soon as you press "create HRUs", you are transforming your model from spatial data into virtual grid, which is not associated with actual X,Y coordinates, only their position in the watershed (distance from the stream, how it is connected to other objects, etc.).
If you want to add the data to a "coordinate", then you need to do so at the data preparation stage. Determine which soil type has this nutrient information and add it in the initiation file for that soil type.
All the best,
Natalja