Moveit planning groups explanation

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I am working on a 6 DOF arm with an end effector attached to it. I have followed the moveit tutorials to configure the arm. But in the planning group tab of moveit setup assistant, there are various options to add such as joints, links, chains and sub-groups. But there are no documentation or tutorials on these topics. So , I have some questions to be answered.

1. In the moveit tutorials for PR2, they have used joints and links to configure the manipulator. But in this tutorial given in 'Mastering ROS for Robotics Programming', they have used kinematic chains instead of joints. So, it is very confusing when to configure the arm as joints and when to configure the arm as kinematic chains.
2. When to use sub group and when to add a new group. Does gripper should always be added as a new group?
3. My ultimate aim is to configure the arm to move it from one point to another point having the end effector in a particular orientation. The gripper/end effector is attached to the link_6. So should I need to define the solver for gripper group or not needed for this group.?

Can anyone shed light on these topics ?