Hello Stasia!
Yes, what you have done is perfectly fine.
You could rig the whole character with the FreeStyle Rigging tool, then distribute all the MTs to layers.
Then rename those layers to MagnetTargets. As long as the layers are called MagnetTargets all will work.
If you need, you can also tween the Magnet Targets to match your symbol's content.

And also, you can label them by entering the MT symbol, adding a layer and typing text. Just do it from frame 2 onward, and then for the individual MTs choose different frames.
If you don't need to tween them, labeling may be a simpler way to identify them, compared to separating them on layers.

This video may also be informative:
Best regards!