Well...its been a few years...but here we go.
It is an old Naval tradition to run up the largest national ensign when going into battle. Usually, this is one of the 'holiday colors', normally flown on Sunday and holidays while inport. This flag is much bigger than the regular colors. Not every captain did it...but those with a certain panache (You know...cojones?) did so.
Normally while underway, the colors or national ensign is usually flown from a 'stick' on the foremast. This 'stick' is really nothing more than a short yardarm that is angled up and aft. It's sole purpose is to support Old Glory. I have seen a ship run up a couple of more regular sized flags from the port and starboard yardarms of the foremast when charging into harm's way. The tradition goes way back to the days of sail in the British Royal Navy. It really looks cool, seeing a destroyer cutting through the water with a bone in her teeth, battle flags whipping in the breeze and the guns blazing away, leaving a series of smoke clouds astern as she races along, pouring out salvos every few seconds. (I did love the smell of cordite in the morning.)
Other flags and shapes are used for different purposes such as to send messages to other ships, designate that ship as the flagship, and to report the status of the ship, such as when taking on fuel or ammunition (Bravo flag), coming alongside (India), or messing around with aircraft (Fox). When a Navy signalman hooks up a flag to be run up, he "bends it on" the signal halyard (rope going up to the yard), then he puts the signal "at the dip" (half way up), or "closes it up", (all the way up to the top of the yard.) When ordered, he "hauls down" the signal.
Clear? Probably about like thick mud.
Gitmo? Yuck!
[beer]