Sorry If this a really dumb question but I have always wondered about this.

When you find some rock piles or some submerged timber on your graph, where exactly is it located?
Directly under your boat? Does the transducer send signals directly down?

Depends if you are using down-imaging or side-imaging. Regular sonar will shoot directly down, shaped like a cylindrical cone, and side-imaging will shoot out horizontally both left and right of the boat.

So if your using down scan imaging and you fond some structure, you need to reposition yourself to where the structure is directly in front of you rather than above it?

Yes, the downscan will shoot directly below where your transducer is. back off 20 or 30 yards and cast onto the structure. I advise you to mark the structure with a marker buoy when directly over it then back off and cast onto it.

Also keep in mind that the deeper the water is, the wider the cone gets... so the structure you're seeing might not be exactly under the boat, but a few feet to the left or right.