A wooden Wayfarer will float if the buoyancy compartments/lockers are flooded. But it will be impossible to recover the boat without beaching it. Float in this context means it will not sink.
You should test that the buoyancy compartments are sound. As a failsafe you can put buoyancy bags in there as well. Under the side bench is not necessary, and would be better off in the buoyancy compartment where the buoyancy is designed to be.
But if the buoyancy compartments/lockers were totally flooded the two bags as you describe them would be woefully inadequate. The compartments are that size for a reason.
If the seals look dodgy then best to replace them, and check carefully that the catches are in good order.
For seals try http://www.porters.org.uk/spare%20parts.htm or perhaps
http://shop.trident-uk.com/acatalog/Wayfarer_Hatches_Fastenings_Fixings.html
You can get seals from all sorts of places – but the right one is a minefield – which does not necessarily mean the same as you have at the moment!.