I would still keep 2 boxes, even if they're side by side. It's good to have a litterbox per cat. If one cat is using the litterbox and the other has to go you can have accidents. It also means each box will stay cleaner and the cats will be more likely to use it.
It may not be a huge issue right now, but once the kitten is an adult the box will get soiled more quickly and if it's not clean enough to their liking one of them may go somewhere else.