When you play Tatooine hunt, teams are named Jawas and Tuskens. I cannot seem to find the strings in the localize tool that lead to those names. Do they have to be manually created, if so what part of localize tool to add in? Thanks.

It's in the LUA file for Hunt. The same function is done for all Hunts.

SetTeamName(2, "Geonosians")

From the Geonosis hunt lua.

I assumed that those lines had a localization string behind them, to present things like Geonosians. Perhaps anything can be put there? Will try later and report back.

EDIT: Nope, I named my two sides using Good and Bad and when the game loads both say Jawas.

I don't remember exactly how i did it, but you can find the names under entity.tat.inf_jawa. And i have some additional keys entity.rrl.inf_ep2_rifleman, entity.rrl.inf_ep2_jettrooper, entity.rrl.inf_ep2_commander.
These are my custom locals. In the lua they are called locals and clone, but ingame the names Jawa and Clone are displayed. So i think the game doesn't care about the name in the lua.

Try to add under entity a new scope with the name of the lvl where your side are munged and under this scope you add keys with the troopers req name.