for ALEX:
See the beginning of Alexander EB. Afaik you also have to change the shortcut to:"RomeTW-ALX.exe" -mod:eb -show_err -nm -noalexander
for BI:
See here. Didn't work for me though, as installer didn't work properly - but maybe it's my pc somehow.
Or here. Worked for me, though only uses the BI.exe to improve AI behaviour (= more naval invasions for example), so there are no 'new' BI features in EB such as: shield wall, swimming, night battles or hordes, religion etc.
Note: Just in case it's best to backup your entire EB folder in "Rome - Total War" before using any of these.