Some rats are naturally inclined to be clean with their poop and some are dreadful. My friend insisted her rats were hopeless with their poop but after a 3 week stay with me I have them perfectly litter trained. Turned out the tray they were using was too big and easy to move around / tip over / proved more fun for digging opportunities. I replaced that tray with a neat heavy ceramic corner bowl and filled it with litter and existing poops whilst keeping everywhere else spotless. Food and water was available on the higher levels and all poop fell down below and was scooped up into their new toilet. Now they are excellent and to my amazement will climb down to the lowest floor just to do their poop.
The same trick worked for my boys except when they're on the higher levels. They are far too lazy to walk down to their ceramic toilet below and poop right next to their plastic litter trays scattered about on the higher levels. They keep their food in the spotless upper litter trays. Well whatever works for them - as long as I know their poop spots it makes my life easy.
