Dear Usman,
I think the important point to mention is if you want to try these fluxes as parameters or as observations.
If you want to threat them as parameters, i.e. calibrate the boundary fluxes, this is only possible via IFM programming (see previous posts).
If you want to threat the values as observations, this is already implemented in the FePEST interface (after FEFLOW 6.2. patch 5). In the FEM you would need to define the budget groups by activating "Budget Charting Mode" in a nodal selection. Subsequently in FePEST, you can declare these groups as observation definitions.
Regards,
Carlos