Hello dressler1,
Sounds like a MODFLOW model ;)
However, for the import of initial heads in FEFLOW I would recommend the following: Save the initial values in a database (.dat f.e.) containing x,y,z (z being the head). Then add the database as a map and establish a parameter link on the hydraulic head, linking the z values with the hydraulic heads. Choose an appropriate interpolation method, i.e. neighborhood relationship when you have dense data already matching with the current mesh.
In the last step, select all nodes where you want to specify the initial heads and assign the values with the link you created.