It is almost impossible to be completely done. My three are pretty good about only using their litter boxes, but guinea pigs poop and pee where they sleep regardless of litter-training. I am pretty sure that they use the restroom while they sleep (someone please confirm this) which is why you cannot prevent it from happening. What kind of bedding do you use? You may not be seeing pee marks in their bedding.
In terms of tips, you can pick up the poops that they make outside of the litter box and place them inside of the litter box. You can mark and reward (congratulate the piggy for going in their litter box with a piece of veggie).
Just please keep in mind that if they are pretty well litter-trained now, they will likely grow out of it. Mo and Stubbins would only go inside of their litter box (aside from under hideys) at one point. They actually grew out of it, though. From my experience, young piggies are more curious, which makes attempting to litter train seem easy, but by the time they reach their teenage months, keeping up with their litter habits is almost impossible!
I hope that this helped!