At the same time, it's annoying to realize that you've made way too many of something that you can't use again. (One solution that I've found for this is to sell the extras on etsy.)
The best solution is to plan well so that you don't have too many of anything, but that's sometimes easier said than done. One way to do it is to cut lengths of parchment paper or bubble wrap to the size of the surface that's going to be covered to use as a guide.
For a recent cake that needed a lot of tiny flowers on two tiers, I used bubble wrap and cut 4" strips that would add up to the perimeters of the tiers that were going to be covered. I made the flowers and put them on the bubble wrap, so that when the strips were covered I knew that I'd have enough but not too many. I wanted them to dry with a slight curve, which is why I used the bubble wrap and not parchment.
By doing this I was able to avoid running out of flowers, and it made the decorating much easier.