It's in the skill_tree.lub file.
The slots start from left to right from
[0]
[1]
...
You can count them and add it to the right slot. As for the misc skill tab. I think it's there in the same file. I haven't made any misc skills yet so I don't know.
I remember you posted the error crash on discord yesterday.
It's probably because your map files aren't right? Did you follow all the steps involved in adding the custom map?
I'd say you start looking at your
mall_aretno.rsw and gat files.