While "Small Boat Handling" is perfectly adequate for, well, handling small boats, it'd likely be less than useful for handling something larger.
Seamanship is the ability to handle vessels that aren't "small watercraft" - anything from a tugboat to an aircraft carrier - and do it in a seaway.
Sample tasks:
Know how to handle a large vessel in restricted water without grounding (Normal - more difficult depending on conditions)
Knowing how to rig a vessel for sea
Knowing how to rig a vessel for a storm
Knowing how to handle a large vessel in a combat situation.
This is, by nature, a little abstract - handling a vessel, from a sailing yacht to an aircraft carrier, in the open sea is a complex undertaking that will naturally need to be abstracted for game play purposes (as I attempted to do with the my proposed sailing rules).
At referee's discretion, this can be treated as a cascade skill with Small Boat handling, on a 2:1 basis. This should cascade from Seamanship to Small Boat Handling - but not vice versa. A Supertanker captain can likely handle a recreational fishing boat just fine; the opposite is quite unlikely.