If you want lasting effects then a background script would be best. You'd add this above your 12 turn script.
Code:
; Susa event
monitor_event GeneralCaptureSettlement CharacterIsLocal
and FactionType macedon
and SettlementName Susa
console_command add_money 5000
terminate_monitor
end_monitor
; Turnly tribute
monitor_event FactionTurnStart FactionIsLocal
and FactionType macedon
and I_SettlementOwner Thebes = macedon
and I_SettlementOwner Athens = macedon
and DiplomaticStanceFromFaction greek_cities = allied
console_command add_money 10
terminate_monitor
end_monitor
If you want to give the player the choice with the Capture_Greece event then you'll probably want to use an event script - though it can be integrated in the background script with some trouble.
Yes, you can give the other settlements to Macedon using the capture_settlement console command, however it would ejected their garrisons so you'd end up with a lot of Greek armies (or rebel if the faction has been destroyed) around the place.
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