Right, this was an email, so if it looks a bit funny, forgive me.
Ok. The files you need to change are in the 'GameInfo' folder.
They are named like so:
RESEARCHSUBJECT_MAXCAPITALSHIPSTECH0
RESEARCHSUBJECT_MAXCAPITALSHIPSTECH1
RESEARCHSUBJECT_MAXCAPITALSHIPSTECH2... up to level 7, they're for the TEC Empire, the Vasari are PHASE, and the Advent are PSI.
Open number 0 for each race and change this line:
researchModifier
modifierType "CapitalShipMaxSlots"
baseValue 1.000000 <--
perLevelValue 1.000000
to something like 5.000000, or however many capital ship slots you want to begin with. This would give you a starting pop of 5.
Now, in all the other files like the ones labelled above, change this line:
researchModifier
modifierType "CapitalShipMaxSlots"
baseValue 0.000000
perLevelValue 1.000000 <--
to something like 5.000000, or whatever you want. This will increase the pop cap when you research that level in the Logistics tab.
So, basically, if you want to start with 100 pop cap for capital ships, change the first files, the ones ending in 0, to 100.000000.
Hope that all makes sense, good luck.
Edit: Here is how to change the fleet supply:
You need to alter another set of files. Like the others but labeled like so:
RESEARCHSUBJECT_MAXSHIPSLOTSTECH0.entity
RESEARCHSUBJECT_MAXSHIPSLOTSTECH1.entity
RESEARCHSUBJECT_MAXSHIPSLOTSTECH2.entity... etc... up to 7
TECH, PHASE, PSI, as before.
Now, open each one and look for:
researchModifier
modifierType "ShipMaxSlots"
baseValue 100.000000
perLevelValue 150.000000 <-- Fleet Supply
researchModifier
modifierType "IncomePercLost"
baseValue 0.000000
perLevelValue 0.093750 <-- Upkeep Percentage
Just change them in each file, say add 50 to every level's Supply, and take 5% off every Upkeep.
Edit2: Oh, and you need to change the Gameplay.constants file, 3rd line down, it has the maximum ships allowed all together, increase that too.