I'd mark any cover, regardless of whether I saw fish on it or not. They may not be there today, or right then, but that's not to say they won't be on it at another time. And even if there is NEVER any fish on it, if you ever get around to using any of the various trolling methods, knowing where that cover is will help you avoid dragging your baits into it.
First thing to learn & become quick at doing, is to learn the buttons to push to get the waypoint marked. Whether you stop & fish it is up to you & how much time you have to devote to "checking it out". You can always go back and delete a waypoint over cover that is no longer there.
Check your Fish/Wildlife or DNR websites to see if they have placed cover in the lake & posted the GPS coordinates of those spots. They can be manually entered into your unit, then checked out when on the lake. Just be aware of the fact that these coordinates may not be pinpoint accurate, but within 10-20ft of the coordinates given. Commercial GPS accuracy isn't allowed to be as accurate as Gov/Military GPS. And also be aware of the fact that the coordinates are measured from your antenna, not your tranducer ... as well as the fact that DI images can come from any part of the fan shaped span of your sonar ping, and may not be directly under the boat or transducer, but to either side.
... cp