You can't train a chin to poop in a litter pan, only pee train, so putting the poops in the box isn't going to do anything. What you need to do is put peed on shavings in the litter pan, then clean up the pee from everywhere else in the cage, so the only spot that smells of pee is in the litter pan. Most pine pellets are dangerous, unless they are the kind that fall apart to sawdust when wet, most pellets are designed to swell up and absorb liquid, so it will cause a blockage if eaten. You want to use pine or aspen shavings not pellets.
The simplest way I've seen is to start out with the whole cage floor covered in shavings, then figure out which corner(s) they want to pee in and move the soiled litter there if they pee elsewhere. Over several weeks put less and less litter in the cage until you only have it in the corner they pee, and put the pan there. You can then slowly move the pan over time to where you want it, if that spot is not where you want it.
The best disinfectant to use is vinegar, but you do have to make sure you wait for it to be fully dry before putting it back in the cage. Also you need to get the vinegar as deeply soaked into the wood as the pee or you will never get it all cleaned. If the staining is really bad you can also try sanding the shelves down to a clean surface.
One thing to keep in mind though, not all chins catch on to litter training. Also not all chins pick a corner to pee in either, my two will just pee a couple steps to the side of where they are sitting. Litter training is not always something that is quick, sometimes a chin takes to it right away, but some take weeks or months if ever. It's also not uncommon for them to just decide to stop using the litter pan one day for no reason. Personally I tried offering a litter pan but didn't really see it as much of a convince myself, I use fleece and just change it more often, the extra laundry doesn't bother me. Before I used fleece I just used shavings over the whole cage floor.