Playing EB with Barbarian Invasion engine

[d'Arthez]

1) How do I do this? I am guessing I modify the short cut in some way?

Just edit the shortcut. "RomeTW.exe" needs to be replaced by "RomeTW-BI.exe"

2) Improved AI? You mean on the strategy map? Because I thought the EB contained major re-working of the battle map AI.

Yes, on the strategy map. Naval invasions add much to the game.