Hi Thomas,
It is not correct that you set a head BC equal to the topographic level, this would reflect the behavior of a seepage boundary. For an artesian well, the head BC should get a value, which depends on the high pressure located down in the aquifer. I would recommend you the following options:
Head BC -> Pressurized value
Minimum flow-rate constraint = Maximum flow expected through the artesian well in m3/d
Maximum flow-rate constraint = 0 m3/d (avoid possible water inflow).
Depending on the local settings, you may use a discrete feature element (DFE), which can enhance the vertical flow. Thus, the outflow would be mainly dominated by the deeper aquifer and not the shallow locations. Phreatic and piezometric surfaces may be complicated, so the most-correct evaluation can be only reached by using the Richards' approach in FEFLOW.
Regards,
Carlos