[Kelly Pedersen]

I think the answer to questions like this will depend heavily on how important the GM wants to make an invention in the campaign. If it's just supposed to be a background thing, something the character has but doesn't worry too much about, one roll is fine, against whatever skill would be used for the most complex part of the device. In the Nautilus' case, I suppose that probably would be a tie between the batteries and the submarine as a whole, so I'd let the player choose either Engineer (Submarine) or Engineer (Electrical).

However, in cases where the process of invention is going to be more important, the GM can break things down a bit further, to ensure that there's plenty of opportunities to test prototypes, work out bugs, etc. In that case, it's better to treat a big, complex device as several smaller, less-complex inventions. For the Nautilus, I'd probably still rate the batteries as an Amazing invention, but the rest of the sub would probably rate as a few Complex or Average inventions - probably Complex for the basic "submerge and resurface at will" ability, and Average for things like storing air and the motive systems.

Of course, if you're trying to emulate Verne's works specifically, I'd lean more towards the first approach than the second - Verne tends to treat the big vehicle as an established fact in his stories, something to justify the plot, and rarely has the person who designed/built it display other feats of amazing invention. It's been a long, long time since I read 20,000 Leagues Under the Sea, but I don't remember Nemo ever inventing new submarine or battery technology during the actual story.