You may have noticed in my thread where I showed off pictures, that I use both methods, fighters and drones, for this task. I don't know what to tell you; Just for fun, I once did an entire system, and I had to add 70+ waypoints, followed by assigning 70+ fire controls. It is terrible.
However, there are a few simple rules you can implement to avoid this. Only scan bodies that have a gravity of at least 0.02. Otherwise, even if you find something, it will not be in an amount worth your time. So usually, I just enter a system, fire five or so drones on each planet, one for each moon, and let my grav survey fighters find me another jump point, which I follow through and keep exploring.
The reason why I use both methods instead of just one is because of fuel and my current situation. I have 200 million fuel in reserve, and no more sorium to make more. I cannot afford fighters. 10 fighters usually means I have to refuel 1 million fuel for each system, an expense I cannot take, and then I have to go back, and refuel another 10 million on the carrier itself. It is easier for me to lug around a collier that has geo survey missiles/drones, which don't cost me any fuel at all. Well, very little fuel.
You just need to keep in mind the following: Geo Survey drones are slow as f**k. I don't mean speed, I mean 'how long it takes for them to do their thing'. A traditional geo or grav survey has 1 or 2 points per hour, a traditional ship has 4 to 10 points per hour. A drone has a tiny fraction of that. It is very likely that I will explore two full systems before I get a read on the moons, not to mention the planets.
So yeah, it's basically, enter a system, fire drones, and move on.
Plus, the most important reason of all: I never ever put my ships in harm's way. Once I research into Advanced Geo Survey, I tend to put some space onto EM or TH sensors, so that my missiles can spot populations or dormant installations. Very useful. Lets me know when it's time to GTFO.