Hi Davide,
You do not need to wait until the end of the optimisation to see the results. Even before you start the run, you can go to Edit -> Save Parameters in FEM. This will trigger the interpolation using the settings behind the Parameter Definitions, so you can check whether the resulting interpolation fulfil your expectations.
The "patchy" distribution is either attributed to the given range in the variogram, the number of pilot points and/or a combination of these two. If I were you, I would simply increase the number of pilot points (as a test by a factor of 2) and check the results. As a way to debug, FePEST writes in the GUI the average pilot point separation, which should go in accordance with the variogram range.
Cheers
Carlos