I would have said that a whole table is 3/3 and that both tables together are 6/3 and not 6/6 (maybe they'll get it that 6/3 equals to 2). Probably a good idea to explain that the "whole" isn't all pens and bottles but the group of 3 or 6 or 12 or whatever.

Maybe start with explaining from the start what happens if there are 7 bottles, when bottles are counted in the groups of six-packs. How many six-packs can you make from 15 bottles?