So if you have 2 stacks of the same seed in the seed box, for example one stack with 5 cottons seeds and another with 20. When you start planting cotton with the 5 seed stack and when the stack finishes, it disappears from the box, but not from the quick access menu(or how its called?) and because there is another stack it lets you plant more plants without depleting the second stack.  If you have only one stack of seed, after you plant them all, they will disappear from the seed box, but stay in your quick access belt. Any attempt to plant will tell you that it fails, but with a second stack it will let you plant however many you want. Which is not something bad because I find it weird, that you have to chose between the seeds or the fruit or plant. If you break a cotton plant for seeds you wont lose the cotton...  I kind get why its done that way tho.