Bondo has a "Gel" that soaks in better than regular classic bondo. It will penetrate the wood a bit, strengthing it and it will be less likely to crack. It is easy to find... I get it at walmart... it is called bondo gel. It is a bit runny though... not as runny as simple 2 part autobody epoxy, but a bit runny. If you can use masking tape to fill in the sides so that you are only stuffing it in from the top of the crack it will work awesome.
If it is just small cracks the gel won't run. Do a small amount at a time so that you don't get ahead of yourself.
Rick