I designed a lot of PatchAntenna and Inverted-F-Antennas using MWO. In terms of S11, simulated vs measured plots were almost the same. But other parameters need more tuning.
Anyway, if you have just this software is a good starting point for a design. You have to combine more offen the simulation with measurement, which you have to do anyway.
First recommendation is to be careful in specifying the parameters of the enclosure.