Use 'indeed' when you want to emphasize that somebody or some fact/observation is correct.
Rabbit: I am scared of Wolves because they eat rabbits.
Wolf: Indeed, rabbits taste delicious! (^0^)
Student: I should have studied last night for the big test.
Teacher: Indeed. If you studied, you wouldn't have gotten a bad grade.
Use 'actually' when you want to tell somebody that they understood you incorrectly, and you want to correct them.
Baby Rabbit: Mommy, rabbits eat wolves right?
Mother Rabbit: Actually, wolves eat rabbits. ;0
Teacher: You studied for the test last night right?
Student: Actually, I was sick and went to sleep.