The true difference between the two is the addition of a Hydrogen and Nitrogen molecule, as doxylamine succinate is written, C17H22N2O, where as Diphenhydramine is written C17H21NO.
Now the bonds do change when you add the additional molecules. Specifically, the extra Nitrogen attaches more regularly to the Carbon making it more stable.
Doxylamine Succinate is actually more powerful in this regard, because it's less likely to breakdown upon ingestion.
This actually means it might be better than Benadryl in receptor regulation. This also means there's a higher possibility of overdose, and some more severe side effects when taking Doxylamine Succinate.
Still, it will work on the same nuero pathways in your system.