Hi Karanka,
First in FEFLOW, you would need to activate the budget history charting mode in a selection with the spring nodes. Then FePEST can recognize the budget activation and provide the option of creating an "Observation Definition" based on a rate-budget value. At the moment FePEST only supports the budget at the end of the model run or the difference (final - initial). As a first estimate, you may use this option.
You can implement a complete budget calibration via IFM programming. If you have a plug-in, which is able to retrieve the budget fluxes at specific time steps and write them down in a file named ifm.fpo (two-columns format: Obs. Name, Value), then FePEST can read this information and use it for the model calibration. In FePEST, you would need to setup a so-called [color=blue][i][b]IFM-Implemented Observation Definition[/b][/i][/color] with the same number of observations and names.
Regards,
Carlos