Sparrowhawk is right - the order doesn't matter.
And about adding units,
don't modify the BIX in the CIV3PTW folder!.
Instead, make a copy of the Civ3X.BIX and put it in the CIV3PTW\Scenarios folder - then rename that Jerikos Mod (or whatever) and make all changes to that BIX file instead.
Then, when you want to add the units, you create a new Folder in the Scenarios folder and give that the same name as the new BIX file ("Jerikos Mod"), then create an Art folder within that and a Units folder, following the same structure as the general Civ3 folder structure, and just place your unit artwork in there.
I.e. you'll end up having the Trebuchet artwork in a folder with this path:
"..\Civilization III\CIV3PTW\Scenarios\Jerikos Mod\Art\Units\Trebuchet"
Adding them to the general CIV3PTW directories, won't necessarily produce errors, but it might, because you will then be overwriting default files - by placing them in a separate folder, it will be easy as heck to back up your files and to upload your mod to this place, for example
Oh, and if you want to play your mod (I assume you do

), just select Load Scenario, and it should be somewhere on the list.