Boundary model is not coincidental to the watershed

Dear all,

I am trying to set up FEFLOW model for a flat area with complicated river system. Could I create a boundary model which is not coincidental to the watershed? This means that the watershed is partly underlain by an aquifer.

If any, what are the additional data need to be inputted for FEFLOW (e.g, recharge, river water level...)?

Any one can help? Thanks in advance,

Lamm