I haven't done that kind of applique in a long time, but I would save them in a separate box - you never know when just a small piece will come in handy on a future project ... chances are if you are using the material now you like it and will likely use it again.
My newest applique project is a bouquet of balloons (23 of them) about the size of a quarter. I am marking the back of the fabric and cutting out circles (a little each day) and saving them in recycled pill containers. They stack in them very nicely without getting all messed up. When I am ready, I will stitch a running stitch around each one and pull it up around a stencil that can be pressed and start making my blocks. They will all be hand appliqued on so I am not sure how many blocks I will make - we will have to see just how "crazy" I end up getting ... lol But, you cn bet I will save any that do not get used - I may want to do it again some day or share with some other "crazy" person.