So this is the flag of the CSA: http://upload.wikimedia.org/wikipedia/commons/thumb/d/da/Flag_of_the_Confederate_States_of_America_%281861-1863%29.svg/590px-Flag_of_the_Confederate_States_of_America_%281861-1863%29.svg.png And this is one of the Confederte Naval Flag: http://upload.wikimedia.org/wikipedia/commons/thumb/9/9a/Confederate_Rebel_Flag.svg/2000px-Confederate_Rebel_Flag.svg.png How did the second flag come to represent the CSA in popular consciousness?
There is a third case, the Confederate Battle Flag. It was adopted by armies because it is easier to distinguish from the US flag.
I can provide a bit of insight into this.
There were actually three flags of the Confederacy. The first one you linked is the first national flag; the second two are as such:
What you linked above is the second naval jack, which is a specific type of flag that's used on the jackstaff (the foreward-most flagpole) on a ship. The jack is usually the top left quarter of a flag. Here's an example of a ship flying the (former) American naval jack, and here's the British naval jack (the "Union Jack.") The jack is flown at the bow of the ship, and the national flag at the stern.
(British naval ships fly various types of flags, but Great Britain's national flag is the jack of those flags. This is HMS Victory flying the British white ensign at the stern, and the jack from the jackstaff.)
(Not to get too far off topic, but the current American naval jack is this. I have strong feelings, but there's a 20-year-rule in effect here.)
This site, despite its hideous design, has an outstanding database of worldwide flags: http://www.crwflags.com/fotw/flags/us^cv.html
One thing you'll see there is that the naval jack has the same basic form of the battle flag of many various armies in the Confederacy. What we think of as today's "Confederate Flag" most closely resembles the battle flag of the Army of Tennessee; the battle flags of most other Confederate armies were closer to square or only slightly rectangular.
