Well, it's straightforward enough.
Throughout your flight, FS monitors your 'g' levels (i.e. acceleration). You can see for yourself if, during flight, you press shift+z a couple of times.
FSUIPC is a module that takes the FS data and feeds them to FLLogger during all flights. This is how PP registers those penalties.
Usually most g's are experienced during touchdown (unless you fly a fighter that is).
Therefore, be extra careful during landings remeberring to flare adequately so that you bring your bird home nicely without any undue stresses.
Avoiding the 2.5 g's is not very difficult and unless something goes disasterously wrong you won't hit 3.5 g's either.
A general rule is aim for a VFS of 100fpm and if you can't make it, at least contain it to below 500fpm.
Some of the more experienced pilots perhaps have more accurate data to share.
