A noodle can be a number of things. Most commonly is it a food that people cook by putting it in boiling or near boiling water and adding various spices for flavor.

I noodle is also another name for one's brain. So when someone tells you to use your noodle they want you to think about something.

There is also a science of throwing noodles on the wall in order to read them and tell the future.
I suppose this would be using your noodle to examine noodles to determine the outcome of other's noodles.