I think it is savegame compatible, it only makes changes that would otherwise be savegame compatible, as far as I know.

Yes, if your play EB as it's normally installed, you use RTW.exe

Keep in mind that EB was designed and balanced for use without abilities like shieldwall, warcry, etc. Having units with those abilities my break the battle balance. I still really like the idea of having hoplites with shieldwall, basically because the clustered up hoplites just don't "feel real", and certain units, where the unit description talks about a shieldwall (i.e. Milnaht, Helveti Phalanx), but, imo, this mod gives the ability to way too many units, like Hastati, or even assault infantry like the Thureophoroi. I might experiment with reinstalling this mod with shieldwall and then removing it from most units. Shouldn't be too hard, right?