I don't use maksimus's eb so have no idea how it should be installed. If it is done manually, it should be all the same except two points:
1) EB should go as <your steam install dir>\steamapps\common\rome total war alexander\EB
2) to create desktop shortcut, right-click Rome: Total War Alexander in Steam->Create desktop shortcut. Then edit shortcut's target by adding
Code:
-mod:eb -show_err -nm -noalexander