Yes, FEFLOW allows the assignment of variable values for any kind of boundary condition. You may either assign them manually on the base of different nodal selections or you may assignments based on parameter links to external map data.
An efficient introduction into assignments is provided by our Demonstration Exercise:
http://www.feflow.com/uploads/media/feflow-booklet62_01.pdf
Corresponding demo data can be download from our website:
http://www.feflow.com/download.html?&no_cache=1