Individual Mode

In Individual Mode each object of the “Bake List” will generate one texture per pass.
Example: If you have two objects “Cube1” and “Cube2” and two pass “Pass1” and “Pass2”. You will get 4 textures “Cube1_Pass1″,”Cube1_Pass2”, “Cube2_Pass1” and “Cube2_Pass2”

Atlas Mode

In Atlas Mode Objects of the Object List will generate one Single Composed Texture Per Pass.
Example: If you have one job “Job1” with two objects “Object1” and “Object2” and two passes “Pass1” and “Pass2” you will get two textures: “Job1_Pass1” and “Job2_Pass2”

OBS: At the Atlas Mode you can also set a “Target” to the Bake. This is used to bake High Poly to Low Poly objects