A Clouded Look for the Ladder

I know it's a feature they added to Phantom Hourglass, and that might not have made it into The Wind Waker's production, but being able to mark your map would be super useful. I'm not even supposed to be exploring yet (something the King of Red Lions is too keen to remind me of if I stray even a hairsbreadth off course), but I'm coming across things that should be marked. 

Particular among these is a submarine just to the south of Eastern Triangle Island. Along with the towers and rafts, it's another monster den where you can find some form of treasure for clearing it out. This sub housed a bottle, but what has me coloured curious is what's above the chest. 

As with the standard ship hold area, there are raised floors on either end of the room in the sub, and the side you come down has a ladder going to the lower level. The raised floor just behind where the chest appears has no such contrivance, though - unless I missed it. Or maybe it's something to get later in the game. 

It's always The Wind Waker's fine details that elude me.