The important thing is ''not'' to tunnel the ship entrance from the surface. You mine ''to'' the surface from inside, thus leaving an opening deep enough to sail through.
How you get inside doesnt matter. Everything ranging from alternative entries to making temp openings and collapsing them with [[shaker_orb|orbs]] works. All that matters is you mine the cave floor deep enough and then mine straight out. Just make sure you have some means of restoring [[stamina]] nearby, especially to avoid [[drowning]].
Even if you get the entrance wrong on the first try. Do not worry. Simply collapse the tile with an orb or Mag priest and try again.