I am thinking about converting some of my storage areas on my boat into hinged covers. I am looking for some hinges that work from the inside so there won't be anything showing on the outside of the deck. I basically want a flush mount storage covers. What type of hinges should I buy?

Flush Mounted Hinges  

:rimshot:   ;D

Yeah except if you go to lowes.com and search for flush mount hinge you get a bunch of hinges that would have metal on the outside of the box.

Might want to try and look for Piano Hinges.  They are usually flush mount and come in varying lengths.

http://www.iboats.com/Marine_Hinges/dm/cart_id.923910623--session_id.180453740--view_id.257645

How do you envision the installation of the "hinges that work from the inside" ?  

Like the kind of hinges you see on kitchen cabinets. I don't want kitchen cabinet hinges I need some marine grade hinges like that. The type of hinges you see on bass boats.

All the bass boat hatch hinges I have seen are the piano type. The hinge pin is mounted so it is almost flush with the deck and level with the carpet backing. Boats with underseat storage have the seats installed with piano hinges.

If you're talking about home made wood, compartment lid tops, morticing the hinge plates to the tops would give you a near invisible look since you'd barely see the hinge joint above the carpet.  

Piano hinges will work well.  You may have to glue a strip of wood to the bottom of your door and frame so that you can affix the hinge to the edge of those pieces with the hinged edge flush with the surface.

Keep in mind, this coniguration will not allow the doors to open much past 90 degrees.  However, it does add inherent stiffness to the assembly.

You can also recess the pieces to surface mount the hinge, flush with the surface.  Install with the hinge pin down.  This will allow the doors to open a bit more than the edge mount method.

I got some stainless steel piano hinges for a machine at work.

They open about 270 degrees.

I picked them up at a truck supply store.

I think these will be your best bet.

Brute

Look at Lowe's for Non-mortised hinge or butt hinge in stainless steel