Double transforms are probably the single most frustrating thing to deal with when you're first learning rigging. What can be even more frustrating is when these issues pop up after it seems like you've got a perfectly working rig and you just want to clean it up in the outliner!
Fortunately, the issues are almost always in one of a couple of relatively simple categories and you get accustomed to dealing with them fairly quickly. This is a video talking about some of those basic scenarios and some ways to address them. Hopefully enough to help get you started in solving some of the more complex issues you may run into down the line.
Maya/Rigging: Dealing with Double Transforms from zeth willie on Vimeo.