End of Days is contained entirely within its own mod folder (with the exception of the introduction movie) it is therefore compatible on the same installation with any other mod that is also contained solely within it's own mod-folder, e.g. Fourth Age Total War.
If a RTW or BI mod which is not contained within its own mod-folder is installed on the same installation of RTW then it is unlikely that End of Days will perform as designed!
The installation requirements for End of Days state that "Modification must be installed over an unmodified copy of the Rome - Total War, Barbarian Invasion expansion patched to version 1.6". However, IF you already have another mod which you are confident is entirely contained within its own mod-folder on your installation you can still install End of Days to the same installation.
Following the instructions in the read-me will work for this case, but if the other mods' folder is contained within the BI folder following them literally will give you an unnecessary additional copy of the other mod! If you have such a mod installed please follow these steps instead:
Make a new folder called eod within your bi folder. So path is:
C:program files\activision\Rome - Total War\bi\eod
or your equivalent.
Make COPIES* of the following sub-folders from the bi folder:
PASTE* the copies into the new eod folder, you do not need to copy any other folders (e.g. CI) which were installed by previous mods.
*do not use cut or drag functions for this
You can then launch the installer and proceed exactly as per the rest of the instructions.
To anyone who followed read-me instructions with other -mod installed: if you need to reclaim hard disc space, check in your eod folder and see if you have a full copy of the other mod within it. Any sub-folder within the eod folder other than the five listed above should be able to be deleted, if you are at all unsure about deleting a folder re-name it first and test everything still works before deleting it!