In this context, the phrase marker is used to identify a visual symbol placed in the display presentation. By placing a marker on the echo it is regarded as an object that you can act upon. If relevant, you can further classify the object as a target.
The phrase target is used to identify an echo in the display presentation that you wish to act upon. The echo may be from a material item, a shallow, reef or rock, or from fish, fish schools or mammals. You must decide which echoes that shall be classified as targets, and whether you shall start target tracking.