How to add a geometry to an existing feature that was created with NULL geometry?

If you're after a GUI solution, you can use the "Add Part" tool (QGIS >=2.2 only). First, make your layer editable. Then in an Attribute Table select a single row with a null geometry that you want to add a geometry to. Back in the map canvas, select the "Add Part" tool and draw your geometry. The null geometry will be replaced by your newly drawn shape.

You can do this straight in spatialite. Run an UPDATE query each time you have the coordinates available like:

UPDATE point_table 
SET geometry=MakePoint(<your_new_x_coord>,<your_new_y_coord>, SRID)   
WHERE site_id=...;

This can be done from the spatialite_gui, or one of the QGIS database plugins. Does that help?