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Hi Shawnysh,
Joints, Links, Chains and Subgroups represent different ways that you can use to specify which parts of the robot (as specified in the URDF) are part of your current planning group.
Looking at the srdf wiki, you can find some more information on the different types. For instance, notice that when a joint is added, the child link is automatically also included.
A chain is just an easy way to add several joints and links to the srdf without having to manually select all the joints/links in between. It is not advisable to mix different methods in a single group.
Hope that clears things up a bit.
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