Can I suggest that the end of the long VIN number is the best one to use as the four digit number on the chassis will change if you change the chassis while the VIN stays the same.
Calum is spot on, as is the text on the first post in the registry thread.
The VIN under the bonnet/hood is the production number. However, in Morgan fashion, it isn't an exact science and there may be some slight anomalies. It would be incorrect to use the number under the seat or on the chassis.
It should also be noted that the US cars have a slightly different VIN configuration; however, I will post up more when I get more information on the topic tomorrow.