I'm guessing this is used as the casual way of saying "see you later", is there any other use of the word or?
Yes, you can also use it as you would use "later" in English. Later (today) I will go to the city. - Nitaenda mjini baadaye. or in story-telling.
"Later see you later" I dont understand, is it 2 sentences like "Later" and "see you later"?
It means , 1. Later 2. See you later
So it means either 1. or 2. I hope it is clearer now.
Is sounds like Arabic's بداية, beginning(weird...). I read a comment from above and saw a more plausible cognate, بعد. Interesting when you think about it.