Adding Units is the same as adding units in Civ III, so wont mention those steps (such as placing the flcs in folders with the correct ini etc) because I assume you already know how to do this. Load the editor, and insert the unit as you would in a Civ III scenario with the numbers you want and the unit name, etc.
In the units tab, look for a box titled Civilopedia Entry: and it should be empty. PTW requires you to enter a label here that you didnt need in Civ III. To do this, you need to find a file called PediaIcons.txt. There are two of them. You need the one in the \CIV3PTW\Text\, not the one in the main \Civilization III\TEXT\ folder.
This file should open in WordPad (if your not using WordPad, the function in any viewer should be similar). Click the edit menu, then option find and type in #ANIMNAME_PRTO_Isabella and search. It should bring you to a list of animations that look something like #ANIMNAME_PRTO_<Unit Name>. Isabella is the last one on the list. Go to the end of this list and prepare to write you new units entry.
You have to enter a specific entry for each new unit in THIS file location. I have tried placing them elsewhere and have had the game crash occasionally. It has to read #ANIMNAME_ and then whatever the extension that you put in the Civilopedia Entry: (in the Unit tab in the editor). Then, after the #ANIMNAME_<Name> that you gave it, you have to indicate the folder it can be found. Look at the previos examples to get an idea of how this is done. Incase that is confusing here is an example:
I create the unit Panzer II in the editor. I have placed all the animations to make this work in a folder called Second Panzer because I already have a one folder with the name Panzer II. Therefore, the location of my flcs are in:
Civilization III\CIV3PTW\Art\Units\Second Panzer\
In the Civilopedia Entry box for the unit Panzer II I type in,
PRTO_Panzer_II
I then save my .bix file and close the editor and open the file PediaIcons.txt in the CIV3PTW\Text\ folder. I find where all my #ANIMNAME files are and go to the bottom of the list and type in,
#ANIMNAME_PRTO_Panzer_II
Second Panzer
Second Panzer is the name of the folder my icons are located, and PRTO_Panzer_II is the name that I entered in the text box in the editor.
I hope this makes sense. If not, try doing exactly what I described, with the same unit and folder names, and see if it clears things up. Also, look at the pre-made units in the editor and the PediaIcons.txt, it makes it easier to understand.
If your still confused, reply and I will explain better.