Manual trans should have gear oil in it, 80 or 85 wieght
Your tcase can have either gear oil or ATF, but generally you match the trans, so if a leak between the two occur, you dont have contaminated fluids. So you want to drain and refill with gear oil.
As to why you have ATF coming out the breather, my best guess is that it is overfilled... but it could be something else too.