Once your rat is eliminating in the box consistently, keep it clean. Like cats, rats may stop using a dirty litter box. Once a day, dump out the litter box and put down a fresh layer of bedding. Some rat cages are very large and have multiple levels. If your rat has this kind of cage, it's unlikely to go up or down stairs when it needs to use the bathroom. Therefore, keep a litter box on each level of the cage. If you started litter training your rat when it was a baby, it will eventually grow out of its box. A litter box needs to be big enough that your rat can comfortably fit inside. As your rat grows, swap out the litter box as needed.

Summary:
Maintain a clean litter box. Use multiple litter boxes for a cage with many levels. Change the litter box size as needed.