I can imagine the newspaper would be a nightmare to deal with. I assume you were using it in an attempt to protect the trays, but I think it is counterproductive since it would hold the moisture and cause more damage than urine that is allowed to evaporate or be absorbed by the pellets.
My "rabbit partner" uses trays, and she uses pine pellets.
You will need to adjust the amount of pellets used (and their distribution) according to if there is a single rabbit or a doe with a litter. The kits don't have the sense to use a designated potty corner, so the pellets need to be scattered all over the tray as opposed to in only one corner.
You can buy large bags of baking soda at warehouse stores like Costco and liberally sprinkle that in the trays. Food grade diatomaceous earth is also said to cut down on odor.