I thought they just had the one helo

Yeah, so Jesse was hanging around on the ship because... why?? 

They used a rhib to avoid radar. They might have the helicopters from the Chinese ship.

Maybe one of those on Capt. Meylan's destroyed ship were still in usable condition?
Or they took one (or two) from the captured Chinese ship?

Transporter. Scotty is a new member.

They have smaller boats that they use.

As far as the helo, I stopped looking for logic in that one during the first season.