@ Ravenic

Which faction are you playing? The economy in EB needs much more attention than the economy in RTW or most of the other mods due to the high upkeep, low farming levels and comparable smaller cities on game start. I would therefore recommend to start EB with a faction that has (after disbanding uneeded ships and very expensive units like Elephants) no serious financial problems on game start and no major campaigns going on. That would be SPQR, Karthago or the Casse.

As for your specific question on the situation in Greece: Alexander's army was not only paid for by Makedonia and Thessaly but also by the Greek allies. When you control all of Greece in EB, including Makedonia and Epeiros, you'll make tons of money out of mining (very important in EB!) and sea-trade. The towns in Greece are so small and underdeveloped to represent the situation after the Galatian invasion that brought a lot of desctruction to those lands. Playing Greece, Epeiros or Makedonia is therefore not recommended for beginners.