Hi, I assume from your post that you're using BI, please refer to the thread that recently popped to the top of the scriptorium:
https://forums.totalwar.org/vb/showt...05#post1380305
the problem with BI is it is no where near as elegant to -mod as RTW, in RTW you only needed the changed files in the modfolder. BI is already effectively a -mod of RTW though not displayed that way in the shortcuts. Nearly all of the files in the BI folder are required to be transfered into the -mod folder before you can add your own mod stuff.

The way BI -mods are currently working is to copy the entire BI directory into lower level of the directory re-name and install over the renamed directory so you run -mod:bi/mymod as the shortcut

To get the files that have defined path names to divert to your mod folder run a search for files containing bi/ and where appropriate change them to bi/mymod/.
For the bits that are not pathed refer to Dol Guldur's last post in the linked thread about creating mod_0.pak.