The weight is the mashtun empty. The volume is any volume you're comfortable using. Most brewers will just use the capacity of the cooler, but it could also be the volume you're comfortable filling it with. The volume simply sets BeerSmith to alert you when you've exceeded that capacity.
You will want to have two equipment profiles for the different batch sizes. If losses to deadspace and trub are equal for both batch sizes, then you'll have a different Brewhouse Efficiency for each. Your 5 gallon batches will have less BHE, even if both have the same mash efficiency.