Who ever thought that this simple question will bring so many replies...
You can have SDM boot file (DISKBOOT.BIN?) on the smaller partition, whole SDM files structure on the bigger one and additionally CHDK PS.FI2 on the bigger one. This way when your partitions are swapped you could run CHDK and use it to swap them back.
It would be cool to provide very limited, very small CHDK-like PS.FI2 program that can be used only for swapping partitions, that could be added to SDM. Very handy in my opinion.