The independent Pokemon slots are usable, and you don't need the code. You can either have independent icons that CAN still switch in battle, or you can use the ACTUAL independent Pokemon that CANNOT switch. Take a look at the fighter chart you can download in the OP.
The CSS slot data has 2 of each Pokemon. The ID's for the Independent Poke's are the ones with the proper CSS icon, while the trainers poke's are the ones with trainers Icons. Use the ID that lines up with THOSE icons to choose the ones you want. Then you also have to use the independent versions of the CSSSlot config files for independent pokes as well. Those are in the download
So I got the independent pokemon working by putting the ids in and then taking the independent slot configs and putting them into the correct folder. The only problem now is that When I choose pokemon trainer it is just one pokemon that can't be switched. Is that just simply a trade off? I can only have one or the other?