While underground, press Y, select your gems list, select a gem, press A, to bury it. If it's kind of low in number, like 10 up to 20, bury another gem of the same color into the very same spot. You can leave it for a few days or dig it right out at that minute (if you buried more than 2 gems) , and you'll get one gem but larger in size depending on how big the combination or on how many days it was buried.