The performance differences are so minor that you will never be able to tell, really, without a dyno. But, a 6-1 should have a slight emphasis towards low end torque when compared to a 6-2, which would be slightly biased as a high rpm power maker. So if you are building a stroker and buying a new header, maybe a 6-1 would be the way to go, but if you are running a higher revving engine , or a 2.4 liter motor which naturally wants to hit peak HP at higher rpms than a 2.8, and are buying a new header,you might want a 6-2.. Again, the difference is extremely minor and i would suggest that you just go by price.....
Physically, the difference is in the design of the collector....the six individual tubes can either run into one big collector, and then from there to the exhaust pipe, or they can have three tubes into two collectors, and then from there two pipes collected again into one exhaust pipe. I have never installed a 6-2 system but have done many 6-1's and I would suspect that the install is slightly easier, although again the difference is probably very minor.
Again...I would just pick by price. Either one will give you all the benefits of a header. Just make sure you get a 2.5 inch exhaust system, too. That means DON'T get a Monza system!
The comon 6-2 isn't an equal length header, the 6-1 is. Mine came with a 6-2 and I had to fabricate a new Y pipe to have something nice. Some of these come with a 2" exit on the Y pipe and hang dow very low, drags on everything for no good reason. The 6-1 is a nicer header.
That said, if you have a really hot engine, get the nismo race header.