Block the area off to where they are only on the pine pellets for a day or so, and this will force them to use this only for eliminating. Then give them access to a small area of non pellets, and they will want to keep this clean, thereby going to pellets for elimination. You can keep increasing the non pellet area as they continue to go to pellets. I think that when we give them too much free area initially, they get too busy playing, etc. to remember to go back to the pellet box.
I put a couple of poops in the pellet box or a used pee pad under the pellets. This worked well at letting them know where to go.
Do they have something comfy to sleep on/in? Raised cot, dog bed or sm. plastic crate? My puppies loved a small plastic crate the best, I think because it was covered and several would pile up in there, the others slept on a covered foam bed.