Capital ship and fleet supply are treated as research, so they have their own RESEARCHSUBJECT entities for each race and level. For example, TEC capital ship research will be called RESEARCHSUBJECT_MAXCAPITALSHIPSTECH0 through MAXCAPITALSHIPSTECH7, and fleet supply would be RESEARCHSUBJECT_MAXSHIPSLOTSTECH0 through 7. The same holds for the other races.

Each of these files contains the increase in the number of fleet supply/capital ship crew supply points, as well as the upkeep. An example from the TEC first rank of fleet supply research:

researchModifier
modifierType "ShipMaxSlots"
baseValue 100.000000
perLevelValue 150.000000
researchModifier
modifierType "IncomePercLost"
baseValue 0.000000
perLevelValue 0.093750

Which says when you research it, you'll gain 150 fleet supply (you start the game at 100, which is the base, and you increase by 150), and it will eat 9.3750% of your income.

So you can modify either the entire research progression for fleet supply, or you can be lazy and just modify the last research to give however much you want. Cap ship crews works the same way.

Hope this helps